Phylogenetic analysis of rubella viruses found in Morocco, Uganda, Cote d’Ivoire and South Africa from 2001 to 2007

First report of the genomic characterization of rubella viruses circulating in Cameroon

Rubella is an acute and contagious viral infection whose gravidity resides in infection during pregnancy, which can result in miscarriage, fetal death, stillbirth, or infants with congenital malformations. This study aimed to describe the genome of rubella viruses (RUBVs) circulating in Cameroon. Throat swabs were collected from health districts as part of the measles surveillance program from 2010 to 2016 and sent to the Centre Pasteur of Cameroon. Samples were amplified by genotyping reverse transcription polymerase chain reaction (RT-PCR) in the search of two overlapping fragments of the gene that encodes the E1 envelope glycoprotein of RUBV. PCR products were sequenced and phylogenetic analysis was performed with MEGA 6 software. Overall, 9 of 43 samples (20.93%) were successfully amplified and sequenced but only eight sequences could be exploited for phylogenetic analysis with respect to the required fragment length of 739 nucleotides. Analysis of viral sequences from Cameroon with other epidemiologically relevant sequences from around the world showed that all RUBVs belonged to lineage L1 of genotype 1G. Cameroon sequences clustered with viruses from West Africa including Nigeria, Ivory Coast, and Ghana with a percentage similarity of 95.4% to 99.2%. This study will enable an update on the molecular epidemiology of RUBV in Cameroon and help in monitoring circulating RUBV for a better implementation of elimination strategies.

Serological makers of rubella infection in Africa in the pre vaccination era: a systematic review

BACKGROUND

Rubella infections in susceptible women during early pregnancy often results in congenital rubella syndrome (CRS). World Health Organisation (WHO) recommends that countries without vaccination programmes to assess the burden of rubella infection and CRS. However; in many African countries there is limited data on epidemiology of rubella infection and CRS. This review was undertaken to assess the serological markers and genotypes of rubella virus on the African continent in order to ascertain the gap for future research.

FINDINGS

A systematic search of original literatures from different electronic databases using search terms such as 'rubella' plus individual African countries such as 'Tanzania', 'Kenya', 'Nigeria' etc. and different populations such as 'children', 'pregnant women' etc. in different combinations was performed. Articles from countries with rubella vaccination programmes, outbreak data and case reports were excluded. Data were entered in a Microsoft Excel sheet and analyzed. A total of 44 articles from 17 African countries published between 2002 and 2014 were retrieved; of which 36 were eligible and included in this review. Of all population tested, the natural immunity of rubella was found to range from 52.9 to 97.9 %. In these countries, the prevalence of susceptible pregnant women ranged from 2.1 to 47.1 %. Rubella natural immunity was significantly higher among pregnant women than in general population (P < 0.001). Acute rubella infection was observed to be as low as 0.3 % among pregnant women to 45.1 % among children. All studies did not ascertain the age-specific prevalence, thus it was difficult to calculate the rate of infection with increase in age. Only two articles were found to report on rubella genotypes. Of 15 strains genotyped; three rubella virus genotypes were found to circulate in four African countries.

CONCLUSION

Despite variations in serological assays, the seroprevalence of IgG rubella antibodies in Africa is high with a substantial number of women of childbearing age being susceptible to rubella infection. Standardized sero-epidemiological data in various age groups as well as CRS data are important to implement cost-effective vaccination campaigns and control strategies.

Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012

Molecular data on rubella viruses are limited in Uganda despite the importance of congenital rubella syndrome (CRS). Routine rubella vaccination, while not administered currently in Uganda, is expected to begin by 2015. The World Health Organization recommends that countries without rubella vaccination programs assess the burden of rubella and CRS before starting a routine vaccination program. Uganda is already involved in integrated case-based surveillance, including laboratory testing to confirm measles and rubella, but molecular epidemiologic aspects of rubella circulation have so far not been documented in Uganda. Twenty throat swab or oral fluid samples collected from 12 districts during routine rash and fever surveillance between 2003 and 2012 were identified as rubella virus RNA positive and PCR products encompassing the region used for genotyping were sequenced. Phylogenetic analysis of the 20 sequences identified 19 genotype 1G viruses and 1 genotype 1E virus. Genotype-specific trees showed that the Uganda viruses belonged to specific clusters for both genotypes 1G and 1E and grouped with similar sequences from neighboring countries. Genotype 1G was predominant in Uganda. More epidemiological and molecular epidemiological data are required to determine if genotype 1E is also endemic in Uganda. The information obtained in this study will assist the immunization program in monitoring changes in circulating genotypes.

Rubella virus genotype 1G and echovirus 9 as etiologic agents of exanthematous diseases in Brazil: insights from phylogenetic analysis

The aim of the present study was to identify the rubella virus (RV) and enterovirus (EV) genotypes detected during the Epidemiological Surveillance on Exanthematic Febrile Diseases (VIGIFEX) study and to perform phylogenetic analysis. Ten RV- and four EV-positive oropharyngeal samples isolated from cell culture were subjected to RT-PCR and sequencing. Genotype 1G and echovirus 9 (E-9) was identified in RV- and EV-positive samples, respectively. The RV 1G genotype has been persisting in Brazil since 2000-2001. No evidence of E-9 being involved in exanthematic illness in Brazil has been reported previously. Differential laboratory diagnosis is essential for management of rash and fever disease.

Case report: congenital rubella syndrome: a rare but persistent concern in the United States

In countries such as the United States where rubella virus infections are rare, congenital rubella syndrome (CRS) may not be recognized in a timely manner. However, the syndrome still appears in this country, often in infants of mothers emigrating from countries with absent or suboptimal national vaccination programs. We describe a case of CRS in a term baby born to a recent US immigrant who developed a primary varicella infection in late pregnancy and demonstrated IgG titers to rubella at delivery. At presentation, the neonate had both classical findings as well as less reported vascular and neurological abnormalities seen in infants with CRS.

Molecular epidemiology of rubella viruses involved in congenital rubella infections in São Paulo, Brazil, between 1996 and 2009

Rubella virus (RV) infection during the early stages of pregnancy can lead to serious birth defects, known as congenital rubella syndrome (CRS). This retrospective study was conducted between 1996 and 2009 with surveillance specimens collected from patients suspected of congenital rubella infection (CRI) and CRS. The clinical samples (nine amminiotic fluid, eight urine, eight blood, one conception product, and one placenta) were sent for viral isolation and genotyping. Twenty‐seven sequences were analysed and four genotypes (1a, 1B, 1G, and 2B) were identified in São Paulo that were involved in congenital infection. To our knowledge, this study is the first report that describes genetic diversity of the circulating rubella strains involved in CRI. J Med. Virol. 85:2034–2041, 2013. © 2013 Wiley Periodicals, Inc.

Rubella epidemic in Vietnam: characteristic of rubella virus genes from pregnant women and their fetuses/newborns with congenital rubella syndrome

BACKGROUND

Rubella remains poorly controlled in Southeast Asia, including Vietnam.

OBJECTIVES

The aim of this study was to characterize rubella virus spread in Vietnam during 2011-2012.

STUDY DESIGN

Amniotic fluid, throat swab and placenta samples were collected from 130 patients (110 cases from pregnant women with suspected rubella and 20 cases from fetuses/newborns). Viral RNA was obtained directly from clinical specimens, amplified by PCR, and then the E1 gene containing 739 nucleotides recommended by the WHO to identify the viral genotypes was sequenced.

RESULTS

By screening with real-time PCR, viral RNA was detectable in amniotic fluids from 103 out of 110 (93.6%) pregnant women with suspected rubella and in the throat swabs from all of 20 (100%) fetuses/newborns. In addition, viral RNA was also detected in the placenta from all cases of fetuses/newborns. All of 20 fetuses/newborns presented with congenital cataract. Twenty-four strains with the E1 gene were obtained by PCR. Using phylogenetic analysis with rubella reference sequences, all of the strains were found to be genotype 2B. Interestingly, 94% (30/32) of Vietnamese strains, including 9 strains from the database, formed an independent cluster within the genotype 2B suggesting that indigenous viruses are prevalent in this region.

CONCLUSIONS

Rubella virus identified in Vietnam belonged to the genotype 2B. Importantly, the infection rate of rubella virus in fetuses/newborns was 100% and all of them had congenital cataract. Our results indicate an establishment of rubella prevention in this area is an urgent task in order to improve maternal and child health.

Epidemiological and molecular characterization of rubella virus isolated in São Paulo, Brazil during 1997-2004

Rubella virus (RV) infection during the early stages of pregnancy can lead to serious birth defects, known as the congenital rubella syndrome (CRS). In 2003, the Pan American Health Organization (PAHO) adopted a resolution calling for the elimination of rubella and the congenital rubella syndrome (CRS) in the Americas by the year 2010. Brazil will have implemented the recommended PAHO strategy for elimination and interruption of endemic rubella virus transmission. The characterization of genotypes during the final stages of rubella elimination is important for determining whether new rubella isolates represent endemic transmission or importations. Samples (blood, urine, cerebrospinal fluid, and throat swabs) collected from patients with symptoms suggestive of rubella infection in 1997-2004 were isolated in cell culture and genotyped. Twenty-eight sequences were analyzed and two genotypes were identified: 1a and 1G. The information reported in this paper will contribute to understanding the molecular epidemiology of RV in São Paulo, Brazil.

Phylogenetic analysis of rubella virus strains during an outbreak in São Paulo, 2007-2008

Rubella virus (RV) is an important human pathogen that causes rubella, an acute contagious disease. It also causes severe birth defects collectively known as congenital rubella syndrome when infection occurs during the first trimester of pregnancy. Here, we present the phylogenetic analysis of RV that circulated in São Paulo during the 2007-2008 outbreak. Samples collected from patients diagnosed with rubella were isolated in cell culture and sequenced. RV RNA was obtained from samples or RV-infected cell cultures and amplified by reverse transcriptase-polymerase chain reaction. Sequences were assigned to genotypes by phylogenetic analysis using RV reference sequences. Seventeen sequences were analyzed, and three genotypes were identified: 1a, 1G, and 2B. Genotypes 1a and 1G, which were isolated in 2007, were responsible for sporadic rubella cases in São Paulo. Thereafter, in late 2007, the epidemiological conditions changed, resulting in a large RV outbreak with the clear dominance of genotype 2B. The results of this study provide new approaches for monitoring the progress of elimination of rubella from São Paulo, Brazil.

Genotyping of rubella virus RNA in sera and dried blood spots collected during routine surveillance and in archival sera

Information on the molecular epidemiology of rubella has been valuable in supporting efforts to control and eliminate rubella in several countries. The preferred samples for virus isolation or RNA detection, such as throat swabs, are often not available making it difficult to obtain a robust database of rubella virus sequences. A method for obtaining rubella virus genotypes from more commonly collected samples such as sera or dried blood spots using real-time RT-PCR to screen samples followed by nested set amplification is described. Rubella genotypes were obtained from dried blood spots and recent and archival sera collections. Eighteen percent of the RNAs extracted from the archival sera were real-time RT-PCR positive, and 44% of these RNAs were amplified successfully by nested RT-PCR and sequenced. Implementation of this technique could provide another tool to improve global rubella molecular surveillance.

Phylogenetic analysis of rubella viruses in Vietnam during 2009-2010

Rubella virus (RV) usually causes a mild disease. However, infection during the first trimester of pregnancy often leads to severe birth defects known as congenital rubella syndrome (CRS). Although wild-type RVs exist and circulate worldwide, their genotypes remain unknown in many countries. The aim of this study was to identify the molecular characteristics of RVs found in Vietnam during the years 2009-2010 and to provide the first data concerning RV genotypes in this country. Throat swab samples were collected between 2009 and 2010 from four CRS cases and nine rubella infection cases visiting one Children's Hospital and one outpatient clinic in Ho Chi Minh City. The 739-nucleotide coding region of the RV E1 gene recommended by the World Health Organization was amplified by reverse transcriptase PCR, and the resulting DNA fragments were then sequenced. Sequences were assigned to genotypes by phylogenetic analysis with RV reference strains. RV RNA was detected in 11 clinical specimens. Phylogenetic analysis of the sequences showed that all 11 strains belonged to 2B genotype. Several variations in amino acids were found, among which five changes were involved in the B and T cell epitopes. These data indicate that viruses of genotype 2B were circulating in Vietnam. The increasing information about RV genotype in Vietnam should aid in the control of rubella infection and CRS in this country.

Emergence and continuous evolution of genotype 1E rubella viruses in China

In China, rubella vaccination was introduced into the national immunization program in 2008, and a rubella epidemic occurred in the same year. In order to know whether changes in the genotypic distribution of rubella viruses have occurred in the postvaccination era, we investigate in detail the epidemiological profile of rubella in China and estimate the evolutionary rate, molecular clock phylogeny, and demographic history of the predominant rubella virus genotypes circulating in China using Bayesian Markov chain Monte Carlo phylodynamic analyses. 1E was found to be the predominant rubella virus genotype since its initial isolation in China in 2001, and no genotypic shift has occurred since then. The results suggest that the global 1E genotype may have diverged in 1995 and that it has evolved at a mutation rate of 1.65 × 10(-3) per site per year. The Chinese 1E rubella virus isolates were grouped into either cluster 1 or cluster 2, which likely originated in 1997 and 2006, respectively. Cluster 1 viruses were found in all provinces examined in this study and had a mutation rate of 1.90 × 10(-3) per site per year. The effective number of infections remained constant until 2007, and along with the introduction of rubella vaccine into the national immunization program, although the circulation of cluster 1 viruses has not been interrupted, some viral lineages have disappeared, and the epidemic started a decline that led to a decrease in the effective population size. Cluster 2 viruses were found only in Hainan Province, likely because of importation.

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.

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 viruses isolated in 2008 outbreak in Argentina

BACKGROUND

A rubella outbreak was recorded in Buenos Aires during 2008.

OBJECTIVES

The objective of this communication is to present the genetic and phylogenetic analyses of wild-type RUBV circulating in Buenos Aires during the 2008 outbreak.

STUDY DESIGN

Throat swab samples collected from patients diagnosed with rubella between June 2008 and December 2008 were inoculated in cell culture and 23 isolates were sequenced.

RESULTS

Phylogenetic analysis of the WHO-recommended window (nt 8731-9469) of the E1 envelope glycoprotein was performed and all isolates clustered with the 2B genotype.

CONCLUSIONS

Genotype 2B seems to be endemically circulating in the Southern cone of Latin America, thus causing recent outbreaks.

Re-emergence of another vaccine-preventable disease?-Two cases of rubella in older adults

Unlike its devastating teratogenic effects, post-natal infection with rubella typically causes subclinical or inapparent illness. While rubella has been largely eliminated from the United States following the introduction of an efficacious live-attenuated vaccine in 1969, a small proportion of the population remains susceptible. Recent declining vaccination rates have resulted in a rising incidence of sporadic and outbreak-associated measles, reminding us that an increasing proportion of the population is also susceptible to, and may be reservoirs of transmission for, rubella. We describe two rare adult cases with no clear exposure. These cases serve as a reminder that clinicians should remain vigilant and consider rubella infection in susceptible patients, including older adults, presenting with febrile rash illness.

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.