Identification of three lineages of wild measles virus by nucleotide sequence analysis of N, P, M, F, and L genes in Japan

Measles Outbreak in a Suburb of Tokyo, Japan, in 1998-1999

A 1998-1999 outbreak of measles in Kawasaki City was studied to provide an up-to-date epidemiological understanding of the disease in Japan. 21 of the 69 total patients (30.4%) seen at the hospital were under 1 y of age. None of the 69 patients had received measles vaccine. 43 out of 50 nasopharyngeal swabs subjected to polymerase chain reaction assay (86%) were positive for the hemagglutinin (H) gene. The measles strain isolated from patients was classified as a D3 genotype. Such outbreaks are important epidemiologically, and these findings shed light on vaccination and immunity patterns in this urban population.

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.

Current status of measles in Japan: molecular and seroepidemiological studies

On account of the measles vaccination campaign, with vaccinations carried out on the first birthdays of children, the number of reported cases of measles was reduced to 545 in 2005, which is the lowest so far in Japan. We conducted a molecular epidemiological study of measles virus to determine the circulating measles virus genotypes in Japan since 1984. Different genotypes, C1, D3, D5, and H1, were the major strains isolated in outbreaks in 1984, 1987-1988, 1991-1993, and 2000, respectively. When measles was in the control phase, a sporadic outbreak was reported, but the causative virus was found to be of imported measles virus lineage. We also conducted a seroepidemiological study to investigate the persistence of vaccine-acquired immunity in Himeji City, Japan. Before 1990, vaccine coverage was 84.5% and it increased gradually, to 88.5% in 1991-1995, 92.7% in 1996-2000, and 94.6% after 2000. Measles outbreaks were observed annually before 1978 and in 1980, 1981, 1984, 1990, and 1996; there were no measles cases after 1997 in Himeji City. In 1994-1998, a serological study of 795 sera showed that measles neutralization test (NT) antibodies were sufficiently preserved, even 12 years after the first-dose immunization. In 1999-2003, 26 (3.7%) of 695 sera were negative for NT. The positive rate for measles NT decreased to approximately 90% as the elapsed time after the first-dose immunization increased to 6 or 7 years. The immunity obtained after receiving measles vaccine decays by 6-7 years after the first dose when the measles was controlled. A two-dose schedule of measles vaccine was implemented in Japan in 2006; we should continue molecular and serological surveillance.

A simple method for the detection of measles virus genome by loop-mediated isothermal amplification (LAMP)

Approximately 20,000-30,000 measles patients were reported in a surveillance of infectious diseases because of low vaccine coverage of 80% in Japan. Among them, some were thought to be secondary vaccine failure (SVF) with generally mild or non-typical measles illness and sometimes became a source of further transmission. We have developed a new, sensitive, and rapid method to detect the measles virus genome by reverse transcription loop-mediated isothermal amplification (RT-LAMP). We examined 50 nasopharyngeal secretion (NPS) samples that were obtained during the 1999 outbreak and stored at -70 degrees C and fresh NPS, lymphocytes and sera from 11 patients in 2003. Total RNA was extracted from the samples and subjected to reverse transcription-polymerase chain reaction (RT-PCR) and RT-LAMP. We detected the genomic RNA corresponding to at least 0.01-0.04 TCID50, 30-100 copies in samples by RT-LAMP within 60 min after extraction of RNA, and all four genotypes isolated in Japan were equally amplified. Specific DNA amplification was monitored spectrophotometrically by real time turbidimeter and the quantity of RNA was calculated. Measles virus genome was detected in 44 of 50 stored NPS by RT-PCR and in 49 by RT-LAMP. The vaccine strain was discriminated from wild strains after sequencing the LAMP products. RT-LAMP is a useful rapid diagnostic method for the detection of measles virus without any special apparatus, showing higher sensitivity than RT-PCR, and expected to be applied for hospital-based infection control and for laboratory-based measles surveillance.

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.

Molecular epidemiology of measles virus in Japan

BACKGROUND

Measles virus has been classified into 22 genotypes. The present report examines the molecular epidemiology of measles virus in Japan from 1984 to 2002, and the epidemiological link between imported cases in several foreign countries and Japanese strains was elucidated from the literature.

METHODS

B95a or Vero cells was used to isolate the measles virus. The measles virus genome was amplified in the N and H genes by reverse transcriptase-polymerase chain reaction and were partially sequenced. Phylogenetic analysis of a partial sequence of the N gene, from position 1230 to 1685, of the recent measles strains was performed in comparison with the World Health Organization reference strains.

RESULTS

There were large outbreaks of measles in Japan in 1984, 1987-1988, 1991-1993, and 2001-2002 and each outbreak was caused by a different genotype. Genotype C1 was an indigenous strain for a long period before 1985, while D3 was isolated in 1987-1988 and D5 in 1991-1993 outbreaks. In addition, the Chicago-type D3 caused sporadic regional outbreaks from 1998 to 1999. After 2000, H1 became the dominant circulating strain. It should be noted that the Japanese strains were detected as imported cases by epidemiological linkage in several countries.

CONCLUSIONS

Among the recent circulating strain of measles virus in Japan the genotype H1 was dominant after 2000 and the Japanese strains D3, D5, and H1 were exported to several countries. It is recommended that Japan should adopt a more extensive and active vaccination strategy for measles elimination in line with other countries in the world.

Recombinant measles AIK-C strain expressing current wild-type hemagglutinin protein

We constructed a recombinant measles virus cDNA, pIC-MVAIK-H/87-K, in which the hemagglutinin (H) gene of the AIK-C vaccine strain was replaced by the wild-type (MVi/Tokyo.JPN/87-K: genotype D3) H gene and the remaining genes were the same as the AIK-C vaccine strain. To investigate the feasibility of the recombinant vaccine strain expressing wild-type H protein instead of the AIK-C H protein, we constructed two recombinant measles cDNA, having Leu (small plaque-type) and Phe (large plaque-type) at position 278 of the F protein. Infectious chimeric virus strains, MVAIK-H/87-K/S (small plaque-type) and MVAIK-H/87-K/L (large plaque-type), were recovered, which were designed to induce small (S) and large (L) plaques in Vero cells. The MVAIK-H/87-K/S and MVAIK-H/87-K/L did not grow at 39-40 degrees C, similar to the original AIK-C strain, and retained the temperature sensitivity (ts) characteristics. They did not induce cytopathic effect (CPE) in Vero cells but produced CPE in B95a cells, similar to the current wild-type measles MVi/Tokyo.JPN/87-K. From the results of Western blotting, the mobility of the H protein of MVAIK-H/87-K/S and MVAIK-H/87-K/L was similar to that of MVi/Tokyo.JPN/87-K. Hyper-immune sera raised by MVAIK-H/87-K/S neutralized all types of current wild strains. Thus, the chimeric measles virus expressing the current wild H protein demonstrated wild-type H properties with ts characteristics of the vaccine strain, indicating that the construction strategy of recombinant measles virus can cope with the hyper-mutated measles virus.

Genetic characterization of wild-type measles viruses in Cambodia

Cambodian authorities in collaboration with the World Health Organization (WHO) are implementing a measles control plan in this measles endemic country. Genetic characterization of Cambodian wild-type measles viruses was performed to determine the genotypes involved in outbreaks, and to measure the level of virus circulation in a geographic area just beginning to implement the measles control program. Seventy-two sequences of the C terminus of the nucleoprotein gene of measles virus were obtained from 88 patients. Samples were taken from 35 among 519 outbreaks reported to the Cambodian National Immunization Program between March 2001 and June 2002. The sequences were grouped into 10 lineages which all belonged to genotype D5. The maximum nucleotide divergence was 1.3%.

Genetic and antigenic characterization of measles viruses that circulated in Korea during the 2000-2001 epidemic

Despite the marked reduction in the incidence of measles in Korea by the introduction of measles vaccine, a large measles epidemic occurred during 2000-2001. During the epidemic, more than 55,000 measles cases were reported and at least 7 children were dead. In this study, we analyzed the genetic and antigenic properties of 15 measles viruses that isolated during the epidemic. Sequence analyses of entire hemagglutinin (H) and nucleoprotein (N) genes of the viruses indicated that all Korean isolates had a high degree of homology (>99.8%) when compared with each other. They differed from other wild-type viruses by as much as 6.8% in the H gene and 6.5% in the N gene at the nucleotide level. The deduced amino acid variability was up to 6.4% for the H protein and up to 6.5% for the N protein. Phylogenetic analysis of nucleotide sequences and deduced amino acid sequences of the H and N genes revealed that all Korean viruses were grouped into the genotype H1. This strongly demonstrated that single genotype of measles virus has been circulated in Korea during the 2000-2001 epidemic. Plaque reduction neutralizing antibody titers against vaccine strains, Edmonston and Schwarz, and recently isolated Korean strains were measured using sera from vaccinees and recently infected children. Although sera of recently infected children demonstrated higher neutralizing antibody titers against wild-type strains than against vaccine strains, both sera neutralized both strains and the reciprocal geometric mean titers (GMTs) were not significantly different against both strains.

H1 genotype of measles virus was detected in outbreaks in Japan after 2000

We investigated the molecular epidemiology and biological characteristics of wild measles viruses isolated since 1984 in Japan. The circulating measles virus was of genotype C1 before 1985, D3 from 1987 to 1990, and D5 from 1990 to 1997. It was replaced by the same cluster of Chicago-type D3 strain from 1997 to 1999. In 2000, D5 recirculated with sporadic cases caused by genotype H1. The H1 genotype became dominant in 2001 with a minor distribution of D5. No significant difference was observed in neutralizing titers against C1, D3, D5, and H1 when we used sera having high neutralizing titers. However, some D3 and H1 strains were not completely neutralized with low levels of neutralizing antibody, and maintaining high levels of measles antibodies would be required for the control measles outbreaks.

Update on the global distribution of genotypes of wild type measles viruses

Molecular characterization of measles viruses is an important component of measles surveillance because these studies enhance our ability to identify the source and transmission pathways of the virus. Molecular surveillance is most beneficial when it is possible to observe the change in virus genotypes over time in a particular region. Such information can help to document the interruption of transmission of measles virus and thus provide an important method for assessing the effectiveness of vaccination programs. It is recommended that virus surveillance be conducted during all phases of measles control and be expanded to give an accurate description of the global distribution of measles genotypes. This review provides updated information on the circulation patterns of measles genotypes and examples of the utility of virologic surveillance.

Current status of measles in Japan

Approximately 20,000 to 30,000 cases of measles are reported annually in Japan, although the actual number of measles infections is considered to be five to ten times higher than the number of reported cases. Despite the availability of effective and safe live attenuated vaccines, regional outbreaks in Okinawa, transmission in adults, and secondary vaccine failures continue. Recent advances in molecular technology have contributed to molecular epidemiological studies, new concepts of asymptomatic infection, and the identification of different characteristics among measles virus genotypes. Measles virus strains isolated in Japan since 1984 were classified into the genotypes C1 (-1985), D3 (1985-1990), D5 (1990-1997), and Chicago-type D3 (1997-1999) from the results of sequencing the hemagglutinin gene. After 2000, the D5 genotype emerged, and, recently, the H1 genotype, which is now dominant, was introduced from Korea. Some of the currently circulating wild-types have different characteristics (high growth rate at 39 degrees C-40 degrees C). The cumulative vaccine coverage has reached 81%, but most measles cases involved unvaccinated individuals. Measles is a preventable disease and can be eradicated by increasing the vaccine coverage, and promoting the motivation for vaccination, in accordance with the worldwide measles strategy.

Co-circulation of two genotypes of measles virus and mutual change of the prevailing genotypes every few years in Osaka, Japan

Genotypes of 44 wild-type measles virus (MV) strains isolated in Osaka, Japan, during 1997-2001, were determined based on phylogenetic analyses of a 456-nt 3' terminal nucleoprotein gene sequence with the reference MV strains designated by the World Health Organization. The wild-type MV strains were classified into two genotypes, D3 and D5, recognized as indigenous in Japan. Six of 12 strains isolated in 1997 were classified into genotype D3 and the other 6 into D5. Eleven of 13 strains were D3, and 2 were D5 in 1998. There were no measles epidemics, and no strains were isolated in 1999. Nine of 10 strains were genotype D5, and only one was D3 in 2000, and 9 of 9 were D5 in 2001. These results indicate that the wild-type MV strains classified into genotypes D3 and D5 co-circulated without the complete change of the MV genotype in Osaka, except in 2001. Furthermore, the prevailing genotype was different between 1998 and 2000-2001. Together with a previous report about MV genotype in this area during 1993-1995, these results suggest that the mutual change of the prevailing wild-type MV genotypes between D3 and D5 occurs every few years in Osaka, Japan.

Role of viruses in human evolution

The study of viral molecular genetics has produced a considerable body of research into the sequences and phylogenetic relationships of human and animal viruses. A review of this literature suggests that humans have been afflicted by viruses throughout their evolutionary history, although the number and types have changed. Some viruses show evidence of long-standing intimate relationship and cospeciation with hominids, while others are more recently acquired from other species, including African monkeys and apes while our line was evolving in that continent, and domesticated animals and rodents since the Neolithic. Viral selection for specific resistance polymorphisms is unlikely, but in conjunction with other parasites, viruses have probably contributed to selection pressure maintaining major histocompatibility complex (MHC) diversity and a strong immune response. They may also have played a role in the loss in our lineage of N-glycolylneuraminic acid (Neu5Gc), a cell-surface receptor for many infectious agents. Shared viruses could have affected hominid species diversity both by promoting divergence and by weeding out less resistant host populations, while viruses carried by humans and other animals migrating out of Africa may have contributed to declines in other populations. Endogenous retroviral insertions since the divergence between humans and chimpanzees were capable of directly affecting hominid evolution through changes in gene expression and development.

Detection of measles virus genome in bone-marrow aspirates from adults

We investigated the presence of the measles virus genome in order to identify asymptomatic infections in the adult population. Bone-marrow aspirates were obtained from 179 patients, 20-96 years of age, for the diagnosis of malignant diseases (29 with malignant lymphoma, 28 with acute leukaemia, 21 with myelodysplastic syndrome, five with multiple myeloma and 96 with other diseases). The measles virus genome was detected in 17 (9.5%) of 179 individuals by RT-PCR and 28 (15.6%) through hybridization. The genomes detected in bone marrow were all in the same cluster, D5, the strain circulating during the study period, and no evidence of persistent infection was obtained. We conclude that asymptomatic infections of measles virus are common in adults and the presence of the measles virus genome would not be related to the pathogenesis of illness.

Molecular analysis of measles virus genome derived from SSPE and acute measles patients in Papua, New Guinea

A very high annual incidence of 56 per million population below the age of 20 years for subacute sclerosing panencephalitis (SSPE) has been reported from Papua New Guinea (PNG). In a more recent study, we have confirmed this unusual high incidence for Eastern Highlands Province (EHP) of PNG. In the study, it was observed that the vaccination rate among SSPE patients registered at Goroka Base General Hospital (GBGH) in EHP was higher than that of other infants in the province in recent years. To identify the measles virus (MV) responsible for SSPE in EHP, sequence analysis of hypervariable region of the N gene was performed from 13 MV genomes: 2 amplified from clinical specimens of SSPE patients and 11 from acute measles patients. In 2 cases among the 11 with acute measles, nucleotide sequence of the entire H gene derived from isolated viruses was determined. Both nucleotide sequence and phylogenetic tree analyses showed that the amplified MV cDNAs were closely related to one another and belonged to the D3 genotype though they were different from any previously reported MV sequences. No genome sequences of vaccine strains were detected. These findings suggest that the MV strains prevailing in the highlands of PNG belong to genotype D3 of the MV and this wild-type MV rather than the vaccine strains was likely to be responsible for SSPE in these patients.

Molecular epidemiology of measles viruses in the United States, 1997-2001

From 1997 to 2001, sequence data from 55 clinical specimens were obtained from confirmed measles cases in the United States, representing 21 outbreaks and 34 sporadic cases. Sequence analysis indicated the presence of 11 of the recognized genotypes. The most common genotypes detected were genotype D6, usually identified from imported cases from Europe, and genotype D5, associated with importations from Japan. A number of viruses belonging to genotype D4 were imported from India and Pakistan. Overall, viral genotypes were determined for 13 chains of transmission with an unknown source of virus, and seven different genotypes were identified. Therefore, the diversity of Measles virus genotypes observed in the United States from 1997 to 2001 reflected multiple imported sources of virus and indicated that no strain of measles is endemic in the United States.

Genetic homogeneity of measles viruses associated with a measles outbreak, São Paulo, Brazil, 1997

During a resurgence of measles in São Paulo, Brazil, in 1997, >40,000 cases (peak incidence rate of 246/100,000 inhabitants) and 42 measles-related deaths were reported. Reverse transcriptase-polymerase chain reaction and nucleotide sequencing were used to analyze specimens from patients who had typical clinical measles infection during this outbreak and from six patients who had had measles in 1995 and 1996. Although wild-type measles viruses (genotypes D5 and D6) were present in São Paulo before this resurgence, we detected only D6 viruses. The genotype D6 viruses isolated during this outbreak had identical sequences to genotype D6 viruses isolated in other parts of Brazil and South America in 1997 and 1998, suggesting that a single chain of transmission was responsible. We also identified genotype A viruses in two vaccine-associated cases from 1995 and 1996. Our findings extend the knowledge of the circulation patterns of measles virus in South America, contributing to measles control efforts in the Americas.

Comparative analysis of titers of antibody against measles virus in sera of vaccinated and naturally infected Japanese individuals of different age groups

The anti-measles virus (MV) antibody titers in the sera of vaccinees and naturally infected individuals of different age groups were measured to help assess the efficacy of the current MV vaccination in Japan. Neutralizing (NT) antibody titers induced by vaccination were 2(3.2) times lower than those induced by natural infection and declined significantly by age 20. The once-decreased NT antibody titers of the vaccinees increased 2(3.6) times during their twenties to titers comparable to those of naturally infected individuals of the same age, implying the possible occurrence of natural infection in vaccinees with decreased anti-MV immunity. Although the current field strains in Japan, types D3 and D5, were reported to differ antigenically from each other and from vaccine strains (type A) to some extent, as demonstrated by different reactivities to monoclonal antibodies, the sera of vaccinees neutralized the two types of field strains and the vaccine strain with the same efficiency. This result suggests that the current vaccine strain would be suitable to elicit protection against types D3 and D5, as long as viral antigenicity is concerned. However, when compared at given hemagglutination inhibition titers, NT antibody titers of vaccinees were 2(1.1) to 2(3.2) times lower than those of naturally infected individuals, suggesting a qualitative difference(s) of anti-MV antibodies between the two groups. It should be emphasized that protective immunity induced by the one-dose vaccination currently implemented in Japan may not be strong enough to ensure lifelong immunity. A two-dose vaccination program with higher vaccination coverage needs to be considered in order to effectively control measles in Japan.

Genetic analysis of Asian measles virus strains--new endemic genotype in Nepal

In many parts of Asia measles virus (MV) continues to be endemic. However, little is known about the genetic characteristics of viruses circulating on this continent. This study reports the molecular epidemiological analysis based on the entire nucleocapsid (N) and hemagglutinin (H) genes of the first isolates from Nepal and Taiwan, as well as of recent MV strains from India, Indonesia, and China. Four isolates collected in various regions in Nepal during 1999 belonged to a new genotype, tentatively called D8. Another Nepalese isolate and one from India belonged to genotype D4. The diversity of the Nepalese strains indicated that measles continues to be endemic in this country. The isolate from Taiwan grouped with D3 viruses and one Chinese strain isolated in The Netherlands was assigned to the previously described clade H, known to be endemic in Mainland China. Molecular characterization emerges as an important tool for monitoring virus endemicity and vaccination efforts.

Genetic characterization of contemporary wild-type measles viruses from Vietnam and the People's Republic of China: identification of two genotypes within clade H

Genetic characterization was conducted on 17 wild-type measles viruses isolated near Hanoi, Vietnam, during 1998 as well as on eight viruses isolated in the Hunan, Hainan, Shandong, and Anhui provinces of the People's Republic of China during 1995, 1998, and 1999. Previous studies had shown that, compared to wild-type measles viruses found in other parts of the world, wild-type viruses from China were genetically distinct and comprised a new clade of viruses, clade H. In this study, sequence analyses of the nucleotides coding for the COOH terminal 150 amino acids of the nucleoprotein (N) and the entire hemagglutinin (H) protein indicated that although all of the viruses from Vietnam were members of clade H, they were clearly distinct from the Chinese viruses. With the exception of MVi/Beijing.China/94/1, the Vietnamese viruses differed from all of the Chinese viruses by at least 3.5 and 2.5% at the nucleotide level for the N and H genes, respectively. These data suggest that clade H should be divided into two genotypes with the Chinese viruses placed in genotype H1 and the Vietnamese viruses in genotype H2. Sequence analysis of measles viruses imported into the United States from either China or Vietnam demonstrated that this designation of genotypes will be helpful in future measles surveillance activities.

The genome nucleotide sequence of a contemporary wild strain of measles virus and its comparison with the classical Edmonston strain genome

The only complete genome nucleotide sequences of measles virus (MeV) reported to date have been for the Edmonston (Ed) strain and derivatives, which were isolated decades ago, passaged extensively under laboratory conditions, and appeared to be nonpathogenic. Partial sequencing of many other strains has identified >/=15 genotypes. Most recent isolates, including those typically pathogenic, belong to genotypes distinct from the Edmonston type. Therefore, the sequence of Ed and related strains may not be representative of those of pathological measles circulating at that or any time in human populations. Taking into account these issues as well as the fact that so many studies have been based upon Ed-related strains, we have sequenced the entire genome of a recently isolated pathogenic strain, 9301B. Between this recent isolate and the classical Ed strain, there were 465 nucleotide differences (2.93%) and 114 amino acid differences (2.19%). Computation of nonsynonymous and synonymous substitutions in open reading frames as well as direct comparisons of noncoding regions of each gene and extracistronic regulatory regions clearly revealed the regions where changes have been permissible and nonpermissible. Notably, considerable nonsynonymous substitutions appeared to be permissible for the P frame to maintain a high degree of sequence conservation for the overlapping C frame. However, the cause and the effect were largely unclear for any substitution, indicating that there is a considerable gap between the two strains that cannot be filled. The sequence reported here would be useful as a reference of contemporary wild-type MeV.

Nucleotide sequences of the matrix protein gene of subacute sclerosing panencephalitis viruses compared with local contemporary isolates from patients with acute measles

Measles viruses isolated from brain cells of patients with subacute sclerosing panencephalitis (SSPE) have numerous mutations, especially in the matrix protein (M) gene. To find whether the M genes of these SSPE viruses were mutated randomly or in a pattern, we sequenced this gene from three strains of defective measles virus isolated in Osaka, Japan. We could deduce the sequence of the possible progenitor measles virus for each patient by comparison of the isolate with measles viruses prevailing at roughly the same time and place as the primary infection. Biased hypermutation affected the M genes of all three SSPE viruses, although the molecular mechanisms for the mutations might be various. Replacements of U with C in the plus strand accounted for 76% of all mutations in two of the strains, but in the other strain, replacements of A with G accounted for 52% of the mutations, and the U residues were unchanged.