Molecular epidemiology of rubella by nucleotide sequences of the rubella virus E1 gene in three East Asian countries

Expansion of the measles and rubella laboratory network, India

Objective

To expand the measles and rubella laboratory network of India by integrating new laboratories.

Methods

In collaboration with the World Health Organization (WHO), the Indian government developed a 10-step scheme to systematically expand the number of laboratories performing serological and molecular testing for measles and rubella. The Indian Council of Medical Research and WHO identified suitable laboratories based on their geographical location, willingness, preparedness, past performance and adherence to national quality control and quality assurance mechanisms. The 10-step scheme was initiated with training on measles and rubella diagnostic assays followed by testing of both measles and rubella serology and molecular unknown panels, cross-verification with reference laboratories and ended with WHO on-site accreditation.

Findings

After extensive training, technical support, funding and monitoring, all six selected laboratories attained passing scores of 90.0% or more in serological and molecular proficiency testing of measles and rubella. Since 2018, the laboratories are a part of the measles and rubella network of India. Within 12 months of initiation of independent reporting, the six laboratories have tested 2287 serum samples and 701 throat or nasopharyngeal swabs or urine samples.

Conclusion

The process led to strengthening and expansion of the network. This proficient laboratory network has helped India in scaling up serological and molecular testing of measles and rubella while ensuring high quality testing. The collaborative model developed by the Indian government with WHO can be implemented by other countries for expanding laboratory networks for surveillance of measles and rubella as well as other infectious diseases.

Characterization of rubella virus genotypes among pregnant women in northern Vietnam, 2011-2013

Rubella virus (RV) infection is an unresolved clinical complication that affects children in developing countries including Vietnam. RV infection during the first trimester of pregnancy causes severe birth defects known as congenital rubella syndrome. This study reports on the genomic characterization of RV strains circulating in northern Vietnam during 2011-2013. RV-IgM positive amniotic fluid specimens were collected from 38 women from northern Vietnam who presented with clinical rubella at the National Hospital of Obstetrics and Gynecology in Hanoi, Vietnam. The RV genes were determined by nested PCR with primers amplifying the 739-nucleotide coding region of the E1 gene. The sequences from the amplified DNA fragments were phylogenetically analyzed and compared to reference RV strains. Seventeen out of 38 samples are positive for RV detecting. All new RV isolates are clustered to genotype 2B. Eighteen amino acid mutations were found in the T and B cell epitopes. These results suggest that genotype 2B RV strains frequently circulate in northern Vietnam. These data describe the RV genotype in Vietnam with the aim of improving maternal and child health in this country.

Phylogenetic Analysis of Envelope Glycoprotein (E1) Gene of Rubella Viruses Prevalent in Japan in 2004

We performed a molecular epidemiological study on the envelope glycoprotein gene (E1 gene) obtained by PCR amplification from specimens of 17 rubella patients in certain areas (Gunma, Saitama, and Kagoshima prefectures, and Tokyo metropolitan area) in Japan in 2004. In these sequences of partially amplified DNAs (283 bases) within the E1 gene, no nucleotide substitution was observed. They were classified into genotype 1D of clade 1 in the constructed phylogenetic tree. One amino acid substitution was found between the amino acid sequence predicted from these DNAs and those of Japanese strains [To-336 vaccine strain (To-336 vac) and its wild progenitor (To-336 wt)]. The results suggest that the rubella viruses (RV) prevalent in certain areas of Japan in 2004 were highly homologous and were closely related with Japanese vaccine strain.

Phylogenetic analysis of rubella viruses involved in congenital rubella infections in France between 1995 and 2009

Rubella is an acute infectious disease that normally has a mild clinical course. However, infections during pregnancy, especially before week 12 of gestation (WG), can cause severe birth defects known as congenital rubella syndrome (CRS). The aim of this study was to perform genotyping and molecular characterization of rubella viruses involved in congenital infections in France over the past 15 years (1995 to 2009). Amniotic fluid (AF) specimens (n = 80) from pregnant women with congenital rubella infections (CRI) before week 20 of gestation, and a few other samples available from children/newborns with CRS (n = 26), were analyzed. The coding region of the rubella virus E1 gene was amplified directly from clinical specimens by reverse transcriptase PCR, and the resulting DNA fragments were sequenced. Sequences were assigned to genotypes by phylogenetic analysis with rubella virus reference sequences. Sufficient E1 gene sequences were obtained from 56 cases. Phylogenetic analysis of the sequences showed that at least five different genotypes (1E, 1G, 1B, 2B, and 1h) were present in France and were involved in congenital infections, with a strong predominance of genotype 1E (87%). This is one of the very few comprehensive studies of rubella viruses involved in CRI. The results indicated that over the past 15 years, multiple introductions of the dominant genotype E caused most of the CRI cases in France. A few sporadic cases were due to other genotypes (1B, 1G, 1h, 2B).

Rubella virus genotypes in the People's Republic of China between 1979 and 2007: a shift in endemic viruses during the 2001 Rubella Epidemic

The incidence of rubella cases in China from 1991 to 2007 was reviewed, and the nucleotide sequences from 123 rubella viruses collected during 1999 to 2007 and 4 viral sequences previously reported from 1979 to 1984 were phylogenetically analyzed. Rubella vaccination was not included in national immunization programs in China before 2007. Changes in endemic viruses were compared with incidences of rubella epidemics. The results showed that rubella epidemics occur approximately every 6 to 8 years (1993/1994, 2001, and 2007), and a shift of disease burden to susceptible young adults was observed. The Chinese rubella virus sequences were categorized into 5 of the 13 rubella virus genotypes, 1a, 1E, 1F, 2A, and 2B; cocirculations of these different genotypes were found in China. In Anhui province, a shift in the predominant genotype from 1F and 2B to 1E coincided with the 2001 rubella epidemic. This shift may have occurred throughout China during 2001 to 2007. This study investigated the genotype distribution of rubella viruses in China over a 28-year period to establish an important genetic baseline in China during its prevaccination era.

Phylogenetic analysis of rubella virus strains from an outbreak in Madrid, Spain, from 2004 to 2005

An outbreak of rubella affected 460 individuals in 2004 and 2005 in the community of Madrid, Spain. Most of the patients were nonvaccinated Latin American immigrants or Spanish males. This study presents the first data on rubella virus genotypes in Spain. Forty selected clinical samples (2 urine, 5 serum, 3 blood, 2 saliva, and 28 pharyngeal exudate samples) from 40 cases were collected. The 739-nucleotide sequence recommended by the World Health Organization obtained from viral RNA in these samples was analyzed by using the MEGA v4.0 software. Seventeen isolates were obtained from 40 clinical samples from the outbreak, including two isolated from congenital rubella syndrome cases. Only viral RNA of genotype 1j was detected in both isolates and clinical specimens. Two variations in amino acids, G253C and T394S, which are involved in neutralization epitopes arose during the outbreak, but apparently there was no positive selection of either of them. The origin of the outbreak remains unknown because of poor virologic surveillance in Latin America and the African countries neighboring Spain. On the other hand, this is the first report of this genotype in Europe. The few published sequences of genotype 1j indicate that it comes from Japan and the Philippines, but there are no epidemiological data supporting this as the origin of the Madrid outbreak.

Genomic analysis of diverse rubella virus genotypes

Based on the sequence of the E1 glycoprotein gene, two clades and ten genotypes of Rubella virus have been distinguished; however, genomic sequences have been determined for viruses in only two of these genotypes. In this report, genomic sequences for viruses in an additional six genotypes were determined. The genome was found to be well conserved. The viruses in all eight of these genotypes had the same number of nucleotides in each of the two open reading frames (ORFs) and the untranslated regions (UTRs) at the 5' and 3' ends of the genome. Only the UTR between the ORFs (the junction region) exhibited differences in length. Of the nucleotides in the genome, 78% were invariant. The greatest observed distance between viruses in different genotypes was 8.74% and the maximum calculated genetic distance was 14.78 substitutions in 100 sites. This degree of variability was similar among regions of the genome with two exceptions, both within the P150 non-structural protein gene: the N-terminal region that encodes the methyl/guanylyltransferase domain was less variable, whereas the hypervariable domain in the middle of the gene was more divergent. Comparative phylogenetic analysis of different regions of the genome was done, using sequences from 43 viruses of the non-structural protease (near the 5' end of the genome), the junction region (the middle) and the E1 gene (the 3' end). Phylogenetic segregation of sequences from these three genomic regions was similar with the exception of genotype 1B viruses, among which a recombinational event near the junction region was identified.

Genetic analysis of rubella viruses found in the United States between 1966 and 2004: evidence that indigenous rubella viruses have been eliminated

Wild-type rubella viruses are genetically classified into 2 clades and 10 intraclade genotypes, of which 3 are provisional. The genotypes of 118 viruses from the United States were determined by sequencing part of the E1 coding region of these viruses and comparing the resulting sequences with reference sequences for each genotype, using the Bayesian inference program MRBAYES. Three genotypes of rubella viruses were found in the United States too infrequently to be considered for indigenous transmission. A fourth genotype was found frequently until 1981, and a fifth genotype was found frequently until 1988, but neither was obtained from nonimported cases after 1988. A sixth genotype was found frequently during 1996-2000, likely because of multiple importations from neighboring countries. The results of the present genetic analysis of rubella viruses found in the United States are consistent with elimination of indigenous viruses by 2001, the year when rubella was considered to be eliminated on the basis of epidemiological evidence.

Molecular epidemiology of rubella virus in Asia: utility for reduction in the burden of diseases due to congenital rubella syndrome

BACKGROUND

Rubella is a mild disease mainly of infants, involving a rash and a fever. However, when women who have no immunity to rubella are infected during the early stage of pregnancy, their babies are often born with congenital rubella syndrome (CRS), which is characterized by a few disorders including deafness, cataracts and heart malformations. To prevent CRS, several strains of live attenuated rubella vaccine have been developed and introduced into immunization programs in many countries. In most Asian countries except Japan, Singapore and Taiwan, rubella remains uncontrolled, and the burden of diseases from CRS is high. In order to develop a control program to reduce the number of CRS cases in Asian countries, it is necessary to conduct a survey of rubella and CRS cases, and to then determine the genotype of the circulating rubella virus in each country.

METHODS

Cases of rubella and CRS, based on national reporting systems or active surveillance in the Asian countries, are summarized. Sequences of the E1 gene of the virus isolates from the Asian countries were compared by phylogenic analysis.

RESULTS

Recent studies of the molecular epidemiology of rubella virus worldwide revealed that there are two genotypes, and that genotype I is circulating almost worldwide, while genotype II is an Asian prototype restricted to the Asian continent. Genotype I viruses fall into a number of groups, some of which are geographically localized. Antigenically these two genotypes are cross-reactive and immunization with either virus results in immunity to all rubella viruses.

DISCUSSION

The hypotheses that rubella virus has evolved on the Asian continent is proposed. The World Health Organization (WHO) has recognized that a rubella immunization program can be combined with the measles immunization program. Inclusion of rubella in the expanded program of immunization (EPI) of measles would be ideal in Asian countries, as it would be efficient and cost effective to administer one injection containing a three-combined vaccine (MMR). It would also be desirable given that WHO require laboratory tests to confirm the presence of measles or rubella as part of it's measles control project, because rubella is often misdiagnosed as measles.

Global distribution of rubella virus genotypes

Phylogenetic analysis of a collection of 103 E1 gene sequences from rubella viruses isolated from 17 countries from 1961 to 2000 confirmed the existence of at least two genotypes. Rubella genotype I (RGI) isolates, predominant in Europe, Japan, and the Western Hemisphere, segregated into discrete subgenotypes; international subgenotypes present in the 1960s and 1970s were replaced by geographically restricted subgenotypes after approximately 1980. Recently, active subgenotypes include one in the United States and Latin America, one in China, and a third that apparently originated in Asia and spread to Europe and North America, starting in 1997, indicating the recent emergence of an international subgenotype. A virus that potentially arose as a recombinant between two RGI subgenotypes was discovered. Rubella genotype II (RGII) showed greater genetic diversity than did RGI and may actually consist of multiple genotypes. RGII viruses were limited to Asia and Europe; RGI viruses were also present in most of the countries where RGII viruses were isolated.

The genomic analysis of rubella virus detected from outbreak and sporadic cases in Rio de Janeiro state, Brazil

BACKGROUND

The molecular epidemiology of rubella virus (RV) based on the analysis of the viral E1 gene sequences indicated the existence of two genotypes that differ from each other by 8 to 10% in their nucleotide sequences: genotype I is present in Europe, North America and Asia; and genotype II is present only in Asia.

OBJECTIVES

The purpose of the study was to identify the RV genotypes circulating in Brazil.

STUDY DESIGN

In this study, we analysed 86 clinical samples collected between 1996 and 1999 during a rubella outbreak and from sporadic cases of rubella in Rio de Janeiro State. For the molecular characterisation of RV strains we have used PCR/nested amplification and direct sequencing of a 513-nucleotide region of the E1 gene.

RESULTS

The E1 gene sequences of 14 RVs were obtained and were assigned to two lineages, both within genotype I. The percentage divergence of nucleotide sequence ranged from 3.4 to 5.1% between these two lineages. These results were in agreement with the pattern of variation observed among the sequences obtained from other lineages of RV.

CONCLUSIONS

This work demonstrated that two new lineages of RV circulated simultaneously between the years 1996 and 1999 in the state of Rio de Janeiro. These results provided new approaches for monitoring the progress of vaccination efforts in Brazil.

An RT-PCR assay using oral fluid samples to detect rubella virus genome for epidemiological surveillance

A reverse transcription nested polymerase chain reaction (RT-PCR) method was developed for detecting rubella virus (RV) RNA using primer pairs which targeted a variable region of the E1 gene. RV genome was detected in oral fluid, throat swabs, serum and tissue samples. This is the first report to show that RV genome can be detected in oral fluid samples, including acute cases < or = 2 days after onset of symptoms, which have previously only been used for antibody testing. This suggests that PCR is useful for assisting with early diagnosis when a sufficient IgM response may not have been mounted. The PCR amplicon of 553 nucleotides was also useful for molecular genotyping, which contributes to RV epidemiological surveillance.

Identification of strain-specific nucleotide sequences in E1 and NS4 genes of rubella virus vaccine strains in Japan

Strain-specific nucleotide sequences of E1 and NS4 genes in five strains of a live rubella virus vaccine manufactured in Japan were identified for comparison, using 2389 nucleotides (1443 nucleotides of the E1 gene, 41 of the 3' terminal region following the E1 gene and 905 of the NS4 gene). Sequences of the E1 gene in three strains (Matsuura, TCRB19 and To-336) were identified. Takahashi and Matsuba strains shared common sequences, but were discriminated by the sequence of the NS4 gene. These five strains showed a phylogenetic relationship with the places of their isolation. In a comparative study of three strains with their unattenuated progenitors, the nucleotides in these regions were almost conserved during the attenuation process.