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

The path to eradication of rubella

Since 1969, rubella and its harmful effect on fetuses infected in utero can be prevented by rubella vaccine, usually given in combination with measles vaccine. The rubella vaccine is highly protective both in children and in adults including women intending to become pregnant. Owing to the use of combined measles and rubella vaccines, congenital rubella infection has been eliminated from the Western Hemisphere and nearly all of Europe. Such combined vaccination is now being applied throughout the world, posing the possibility of eventual rubella eradication. The existence of viruses of animals related to rubella does not appear to be a barrier to eradication of the human virus. However, persistent rubella virus in infants infected in utero and of immunosuppressed patients with granulomas may pose a problem for eradication. Nevertheless, this review posits that eradication of rubella is now feasible if routine vaccination of infants and surveillance for chronic infection are correctly applied.

Measles and Rubella Incidence and Molecular Epidemiology in Senegal: Temporal and Regional Trends during Twelve Years of National Surveillance, 2010-2021

We investigated the epidemiology of measles and rubella infections in Senegal based on data from twelve consecutive years of laboratory-based surveillance (2010−2021) and conducted phylogenetic analyses of circulating measles viruses. Sera from measles-suspected cases were collected and tested for measles and rubella-specific IgM antibodies using enzyme-linked immunosorbent assays (ELISA). Throat swabs were collected from patients with clinically diagnosed measles for confirmation by reverse-transcription polymerase chain reaction (RT-PCR) and viral genotyping. Among 8082 laboratory-tested specimens from measles-suspected cases, serological evidence of measles and rubella infection was confirmed in 1303/8082 (16.1%) and 465/6714 (6.9%), respectively. The incidence of rubella is now low—0.8 (95% CI 0.4−1.3) cases per million people in 2021—whereas progress towards measles pre-elimination targets (<1.0 case per million people per year) appears to have stalled; there were 10.8 (95% CI 9.3−12.5) cases per million people in 2021. Phylogenetic analyses revealed that all Senegalese measles strains belonged to genotype B3. The rubella virus sequence obtained in this study was consistent with genotype 1C. Our national surveillance data suggest that despite their low incidence both measles and rubella remain endemic in Senegal with a concerning stagnation in the decline of measles infections that represents a significant challenge to the goal of regional elimination.

Phylogeography of rubella virus in Asia: Vaccination and demography shape synchronous outbreaks

Rubella virus causes mild disease in children but for women in the early stages of pregnancy, it can cause spontaneous abortion, congenital rubella syndrome (CRS) and associated birth defects. Despite the availability of an effective vaccine, rubella virus continues to circulate endemically in several regions of the world. This is particularly true in East and Southeast (E/SE) Asia, where control efforts vary widely among countries that are well connected through travel and immigration. It is therefore important to understand how the regional persistence of rubella is affected both by dynamics occurring across countries and susceptibility within countries. Here, we use genetic and epidemiological data from countries in E/SE Asia to explore the phylogeography of rubella virus in this region. Our results underline that metapopulation dynamics are key for rubella persistence and highlight the source-sink population structure of the region. We identify countries that contribute to the regional metapopulation network and link epidemic dynamics to susceptibility profiles within each country. Our results indicate that human movement plays an important role in driving epidemic dynamics in E/SE Asia.

A novel cell-based high throughput assay to determine neutralizing antibody titers against circulating strains of rubella virus

A large rubella outbreak occurred in Japan 2013, and 14,344 rubella and 45 congenital rubella syndrome (CRS) cases were reported. At that time, the populational immunity was above the protective threshold assessed by hemmaglutination inhibition (HI) titer. The genotype 2B rubella virus (RV) strains were responsible for the outbreak, which are non-indigenous in Japan. In this work, a cell-based high throughput assay was established to measure the neutralizing antibody (NA) titer against circulating RV isolates. RV infection poorly induces cytopathic effects in tissue culture, preventing the casual measurement of NA titer. Our assay system has overcome this hurdle. Using this assay, we re-evaluated the antibody prevalence rate against circulating viral isolates using human sera collected before the outbreak. Individuals with protective IgG titer (≥10 IU/ml) represented 88.1% of the population. Consistently, 85.2% of the population had protective neutralizing antibody titers (≥1:8) against the vaccine strain. In contrast, 50.5% of the population had protective neutralizing antibody titers against circulating genotype 2B RV strains. These data suggest that the herd immunity assessed by HI titer should have been appreciated deliberately.

Epidemiological and molecular investigation of a rubella outbreak, Romania, 2011 to 2012

We describe a rubella outbreak that occurred in Romania between September 2011 and December 2012. During this period 24,627 rubella cases, 41.1% (n=10,134) of which female, were notified based on clinical criteria, and a total of 6,182 individuals were found serologically positive for IgM-specific rubella antibody. The median age of notified cases was 18 years (range: <1-65) and the most affected age group 15 to 19 years (n=16,245 cases). Of all notified cases, 24,067 cases (97.7%) reported no history of vaccination. Phylogenetic analysis of 19 sequences (739 nucleotides each), from 10 districts of the country revealed that the outbreak was caused by two distinct rubella virus strains of genotype 2B, which co-circulated with both temporal and geographical overlap. In addition to the 6,182 IgM-positive rubella cases, 28 cases of congenital rubella syndrome (CRS) were identified, including 11 neonatal deaths and one stillbirth. The outbreak underscores the need to encourage higher vaccination uptake in the population, particularly in women of reproductive age, and to strengthen epidemiological and laboratory investigations of suspected rubella cases. Genetic characterisation of wild-type rubella virus is an essential component to enhance surveillance and here we report rubella virus sequences from Romania.

Genetic diversity of currently circulating rubella viruses: a need to define more precise viral groups

Recent studies have shown that the currently circulating rubella viruses are mostly members of two genotypes, 1E and 2B. Also, genetically distinct viruses of genotype 1G have been found in East and West Africa. This study used a Mantel test to objectively include both genetic diversity and geographic location in the definition of lineages, and identified statistically justified lineages (n=13) and sub-lineages (n=9) of viruses within genotypes 1G, 1E and 2B. Genotype 2B viruses were widely distributed, while viruses of genotype 1E as well as 1G and 1J were much more geographically restricted. This analysis showed that more precise groupings for rubella viruses are possible, which should improve the ability to track rubella viruses worldwide. A year-by-year analysis revealed gaps in surveillance that need to be resolved in order to support the surveillance needed for enhanced control and elimination goals for rubella.

The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates

BACKGROUND

Annually, rubella virus (RV) still causes severe congenital defects in around 100 000 children globally. An attempt to eradicate RV is currently underway and analytical tools to monitor the global decline of the last remaining RV lineages will be useful for assessing the effectiveness of this endeavour. RV evolves rapidly enough that much of this information might be inferable from RV genomic sequence data.

METHODS

Using BEASTv1.8.0, we analysed publically available RV sequence data to estimate genome-wide and gene-specific nucleotide substitution rates to test whether current estimates of RV substitution rates are representative of the entire RV genome. We specifically accounted for possible confounders of nucleotide substitution rate estimates, such as temporally biased sampling, sporadic recombination, and natural selection favouring either increased or decreased genetic diversity (estimated by the PARRIS and FUBAR methods), at nucleotide sites within the genomic secondary structures (predicted by the NASP method).

RESULTS

We determine that RV nucleotide substitution rates range from 1.19 × 10(-3) substitutions/site/year in the E1 region to 7.52 × 10(-4) substitutions/site/year in the P150 region. We find that differences between substitution rate estimates in different RV genome regions are largely attributable to temporal sampling biases such that datasets containing higher proportions of recently sampled sequences, will tend to have inflated estimates of mean substitution rates. Although there exists little evidence of positive selection or natural genetic recombination in RV, we show that RV genomes possess pervasive biologically functional nucleic acid secondary structure and that purifying selection acting to maintain this structure contributes substantially to variations in estimated nucleotide substitution rates across RV genomes.

CONCLUSION

Both temporal sampling biases and purifying selection favouring the conservation of RV nucleic acid secondary structures have an appreciable impact on substitution rate estimates but do not preclude the use of RV sequence data to date ancestral sequences. The combination of uniformly high substitution rates across the RV genome and strong temporal structure within the available sequence data, suggests that such data should be suitable for tracking the demographic, epidemiological and movement dynamics of this virus during eradication attempts.

Analysis of whole genome sequences of 16 strains of rubella virus from the United States, 1961-2009

Rubella virus is the causative agent of rubella, a mild rash illness, and a potent teratogenic agent when contracted by a pregnant woman. Global rubella control programs target the reduction and elimination of congenital rubella syndrome. Phylogenetic analysis of partial sequences of rubella viruses has contributed to virus surveillance efforts and played an important role in demonstrating that indigenous rubella viruses have been eliminated in the United States. Sixteen wild-type rubella viruses were chosen for whole genome sequencing. All 16 viruses were collected in the United States from 1961 to 2009 and are from 8 of the 13 known rubella genotypes. Phylogenetic analysis of 30 whole genome sequences produced a maximum likelihood tree giving high bootstrap values for all genotypes except provisional genotype 1a. Comparison of the 16 new complete sequences and 14 previously sequenced wild-type viruses found regions with clusters of variable amino acids. The 5' 250 nucleotides of the genome are more conserved than any other part of the genome. Genotype specific deletions in the untranslated region between the non-structural and structural open reading frames were observed for genotypes 2B and genotype 1G. No evidence was seen for recombination events among the 30 viruses. The analysis presented here is consistent with previous reports on the genetic characterization of rubella virus genomes. Conserved and variable regions were identified and additional evidence for genotype specific nucleotide deletions in the intergenic region was found. Phylogenetic analysis confirmed genotype groupings originally based on structural protein coding region sequences, which provides support for the WHO nomenclature for genetic characterization of wild-type rubella viruses.

Results of the rubella elimination program in Catalonia (Spain), 2002-2011

Rubella is usually a mild disease with nonspecific symptoms, but can cause congenital rubella syndrome (CRS) when infection occurs during pregnancy. The objective of this study was to evaluate the sensitivity and positive predictive value of different data sources used for surveillance purposes in the Rubella Elimination Program of Catalonia between 2002 and 2011. The Urgent Notification to the Statutory Disease Reporting System, the Individualized Disease Reporting System, screening for other viruses included in the Measles Elimination Program, the Microbiological Reporting System and the Minimum Hospital Discharge Data were evaluated. 100 suspected cases of postnatal rubella and 6 suspected cases of CRS were detected. For postnatal rubella, Urgent Notification had the highest sensitivity (32.5%; 95%CI 18.6-49.1), followed by the Virus screening in Measles Elimination Program (25%; 95%CI 12.7-41.2). Virus screening in the Measles Elimination Program had the highest PPV (76.9%; 95%CI 46.1-94.9), followed by the Individualized Disease Reporting System (57.1%; 95%CI 28.9-82.3). For CRS cases, the Individualized Disease Reporting System had the highest sensitivity (100%, 95%CI 29.2-100) and the highest PPV (60%; 95%CI 14.7-100). Most confirmed postnatal cases (25 cases, 48.1%) were in the 25-44 y age group followed by the 15-24 y age group (11 cases, 21.2%). The highest values of sensitivity and PPV for the detection of confirmed cases corresponded to activities that were specifically introduced in the measles and rubella elimination programs.

Evidence used to support the achievement and maintenance of elimination of rubella and congenital rubella syndrome in the United States

On 29 October 2004, an expert panel was convened to review the status of elimination of rubella and congenital rubella syndrome (CRS) in the United States. Primarily based on 5 types of information presented--epidemiology of reported cases, molecular epidemiology, seroprevalence, vaccine coverage, and adequacy of surveillance--the panel unanimously agreed that rubella virus is no longer endemic in the United States. Since 2004, new data continue to support the conclusion that elimination has been achieved and maintained. In documenting elimination in the United States, each of the 5 types of data provided evidence for elimination and collectively provided much stronger evidence than any one type could individually. As countries document the elimination of rubella and CRS, many sources and types of data will likely be necessary. Rigorous data evaluation must be conducted to look for inconsistencies among the available data. To maintain elimination, countries should maintain high vaccine coverage, adequate surveillance, and rapid response to outbreaks.

Enhanced laboratory surveillance for the elimination of rubella and congenital rubella syndrome in the Americas

One of the reasons the 1997 Technical Advisory Group on Vaccine-Preventable Diseases recommended acceleration of rubella and congenital rubella syndrome (CRS) prevention efforts was the fact that the enhanced measles surveillance system in the Americas found that 25% of reported measles cases were laboratory-confirmed rubella cases. Until 1997, the laboratory network primarily focused on measles diagnosis. Since 1999, due to the accelerated rubella control and CRS prevention strategy, laboratories have supported the regional measles, rubella, and CRS elimination goals. The measles-rubella laboratory network established in the Americas provides timely confirmation or rejection of suspected measles and rubella cases, and determination of the genotypic characteristics of circulating virus strains, critical information for the programs. A quality assurance process has ensured high-quality performance of procedures in the network. Challenges are occurring, but the measles-rubella laboratory network continues to adapt as the requirements of the program change, demonstrating the high quality of the laboratories in support of public health activities and elimination goals.

Persistence and titer changes of rubella virus antibodies in primiparous women who had been vaccinated with strain RA 27/3 in junior high school

Taiwan's rubella vaccination program was launched in 1986; each schoolgirl in the third grade of junior high school received one dose of rubella (RA 27/3) vaccine. We reviewed the results of 14,090 prenatal rubella tests for primiparas from three areas of Taiwan during 2002 to 2008 to investigate seronegativity rates and titer changes. In all primiparous women, the average rubella virus seronegativity rate was 6.5% (95% confidence interval [95% CI], 6.1 to 6.9%), and the average rubella virus antibody titer was 65.9 IU/ml (95% CI, 64.7 to 67.1 IU/ml). There were 1,220 women (8.7%) with weakly positive antibody titers (10 to 20 IU/ml). The rubella virus seronegativity rates, which ranged from 5.4 to 9.7%, did not exhibit a linear trend from 9 to 22 years after vaccination (P = 0.201); in contrast, a significant trend appeared in the average rubella virus IgG titer (P = 0.003), dropping from 69.9 IU/ml in the 9th year after vaccination to 54.8 IU/ml in the 22nd year. The mean annual antibody decay rate was -0.77 IU/ml. This study reveals that the level of rubella virus antibodies declined slowly in women of childbearing age who were vaccinated with RA 27/3 at junior high school age. The number of women who were seronegative or had weakly positive antibody titers was still high (15.2%). Therefore, in countries that implement a single-dose regimen in children or teenagers, it should remain an important policy to encourage voluntary immunization in seronegative women and to immunize all postpartum women who are susceptible to rubella virus infection before they leave the hospital.

Rubella seroepidemiology and estimations of the catch-up immunisation rate and persistence of antibody titers in pregnant women in Taiwan

OBJECTIVE

To examine rubella seroepidemiology, and estimate rates of catch-up immunisation and persistence of antibody titers in pregnant women in Taiwan after mass immunisation.

DESIGN

A retrospective study.

SETTING

Two medical centres and four regional hospitals specialising in obstetric care.

SAMPLE

A total of 43,640 prenatal rubella test results for pregnant women from 2001 to 2008.

METHODS

Rubella immunoglobulin G (IgG) antibody assay.

MAIN OUTCOME MEASURES

Seronegativity, rate of catch-up immunization, and antibody decline.

RESULTS

The seronegativity was 10.9% in all pregnant women. Immigrant women had higher seronegativity than indigenous women (OR 2.86; 95% CI 2.65, 3.01). Indigenous women born prior to implementation of the vaccination programmes were more susceptible (20.1%) to rubella infection than were women born thereafter (6.7%). Rates of seropositive conversion were low in both Taiwanese-born and foreign-born women (11.5 and 30.7%, respectively). The rubella antibody titers for vaccinated Taiwanese women in the 1971-1976 and after-1976 birth cohorts declined by 0.6 and 2.3% per year, respectively.

CONCLUSIONS

This study demonstrates high seronegativity of older indigenous and immigrant women, a low catch-up immunisation rate, and the persistence of rubella antibodies in Taiwan after mass vaccination. Our study suggests that a single dose of rubella vaccine in teenagers effectively increased rubella seropositivity during their childbearing years. This finding is useful for countries that lack the resources necessary for a two-dose regimen. We recommend free rubella antibody tests to women of childbearing age and free vaccination as required. All postpartum women testing negative for rubella antibodies should be vaccinated before they leave hospital.

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.

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.