Measles Virus Genotypes Research Articles

Ecological distribution and phylogenetic diversity of measles virus genotypes in West Africa, 2001 to 2020

Ecological distribution and phylogenetic diversity of measles virus genotypes in West Africa, 2001 to 2020

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

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

Genetic Characterization of Wild-Type Measles Viruses Isolated in Peshawar Pakistan

Background: Measles is a highly contagious disease, caused by the Measles Virus (MV). Knowledge of genotypes prevalent in any region is important in effective measles surveillance; by mapping distribution of prevalent MV genotypes at different points of time, in a region, gives an idea about the success of measles control through vaccination programs, by documenting the interruption of transmission of the endemic viral genotype. Objectives: To detect genotypes of wild type measles virus isolated from the samples collected of measles patients in Peshawar valley of Khyber Pakhtunkhwa (KPK) province, Pakistan.Material and Methods: This was a cross-sectional descriptive study. Nasopharyngeal and/or throat swab samples were collected during a measles outbreak, from February to March 2014, from clinically diagnosed measles patients (cases who met the clinical case definition of WHO). Collection and processing were done according to the standard protocols. RNA (Ribo-Nucleic Acid) was extracted directly from samples; cDNA (Complimentary Deoxy-Ribonucleic Acid) was synthesized, amplification and sequencing of 528bp of carboxy-terminal of N gene was carried out. Sequences were analyzed and data were compared with the standard reference strains of measles virus.Results: A total of nine sequences obtained were of good quality and enough in length to meet WHO criteria for genotype assignment. It was found that all the nine strains of measles virus belonged to clade B, genotype B3 and cluster B3.1. The rest of the 13 sequences which were shorter in length for genotype assignment also showed close resemblance to Genotype B3.Conclusion: Wild type measles virus strains, isolated from the samples of measles patients, in Peshawar valley of Khyber Pakhtunkhwa province of Pakistan were found to be genotype B3. It shows that genotype B3 may be the predominate genotype prevalent in Peshawar region at the time of this study.Keywords: B3 genotype, Genotyping of measles, Measles Virus, Molecular epidemiology.

Genome sequence of a measles virus strain with a novel loss of stop codon mutation in the phosphoprotein gene.

Measles virus genotype B3 coding-complete genome sequence from a 2019 case showed a novel mutation in the phosphoprotein (P) gene that abrogates the established stop codon. A downstream stop codon has been identified, resulting in a putative P that would be 19 amino acids longer than wild type.

Genetic Characterization of the H Gene of MeV Strains (H1, B3, and D4) Recently Circulated in Iran for Improving the Molecular Measles Surveillance in the National Measles Lab.

Despite decreasing the global burden of measles disease after the introduction of vaccination, measles remains one of the most devastating childhood diseases. Since genotype B3 is reported as a predominant Measles Virus (MeV) genotype recently, the current study aimed to better understand MeV genetic variation by analyzing the complete sequence of Hemagglutinin (H) gene associated with outbreaks of circulated genotypes in Iran. Nine positive measles specimens were selected from three circulated different genotypes H1, B3, and D4. Two different regions of MeV RNA were detected by RT-PCR assay. Sequence data and phylogenetic trees were analyzed and constructed by MEGA X software program. Moreover, missense and silent mutations in critical positions of the MeV-H protein were investigated. The result of phylogenetic analysis from the C-terminus of the Nucleoprotein gene (NP-450) and the complete H gene revealed that the mean sequence diversity was 0.06%-0.08% and 0.04%, respectively. Genotype H1 had the highest mutation in this study; however, the substitutions in genotype B3 fundamentally occurred in critical epitopes. Moreover, genotype D4 was more stable than genotypes B3 and H1. Mutations were investigated in the whole sequence of H protein. Moreover, the mutations that occur in the critical sites of the protein have an important effect on the pathogenicity of the virus. In this way, we were able to illustrate why genotype B3 is more transmissible than other measles genotypes and is the most important circulating genotype around the world.

Molecular Epidemiological Study of Measles Cases in Gyeonggi Province

Measles is one of the highly contagious infectious diseases in which about 90% of the groups that have no immunity against measles are infected when exposed to the measles virus. Even after the Republic of Korea was certified as a ‘national measles eradication’ by the WHO in March 2014, two import-related outbreaks of measles occurred in 2014 and 2019. In this study, we analyzed epidemiological characteristics and genetic distribution of measles cases. Ninety-eight nasopharyngeal or oropharyngeal swab samples that confirmed cases of measles in Gyeonggi province in 2019 were conducted genotyping assay and sequence analysis. Fifty cases were classified as group outbreak-related cases and Forty-eight cases were classified as sporadic cases. As a result of genetic analysis, these cases were classified into D8, B3, and A genotypes, and except for the A type which was known as the vaccine type, D8 and B3 types were identified as import-related measles viruses. As with these results, for the complete eradication of measles, not only a high-quality surveillance system but also molecular epidemiological analysis data must be supported. The results of this study are expected to be used as important data for establishing a quarantine system through the accumulation of measles virus genotyping data and case reports data in the future when measles occurs in South Korea.

Correlating IgG Levels with Neutralising Antibody Levels to Indicate Clinical Protection in Healthcare Workers at Risk during a Measles Outbreak.

The rapid transmission of measles poses a great challenge for measles elimination. Thus, rapid testing is required to screen the health status in the population during measles outbreaks. A pseudotype-based virus neutralisation assay was used to measure neutralising antibody titres in serum samples collected from healthcare workers in Sheffield during the measles outbreak in 2016. Vesicular stomatitis virus (VSV) pseudotypes bearing the haemagglutinin and fusion glycoproteins of measles virus (MeV) and carrying a luciferase marker gene were prepared; the neutralising antibody titre was defined as the dilution resulting in 90% reduction in luciferase activity. Spearman’s correlation coefficients between IgG titres and neutralising antibody levels ranged from 0.40 to 0.55 (p < 0.05) or from 0.71 to 0.79 (p < 0.0001) when the IgG titres were obtained using different testing kits. In addition, the currently used vaccine was observed to cross-neutralise most circulating MeV genotypes. However, the percentage of individuals being “well-protected” was lower than 95%, the target rate of vaccination coverage to eliminate measles. These results demonstrate that the level of clinical protection against measles in individuals could be inferred by IgG titre, as long as a precise correlation has been established between IgG testing and neutralisation assay; moreover, maintaining a high vaccination coverage rate is still necessary for measles elimination.

Measles epidemiology and viral nucleoprotein gene evolution in Shandong Province, China.

Measles, caused by measles virus (MeV), has not been eradicated in many regions and countries, threatening human health. Thus, it is beneficial for measles elimination to understand measles epidemiology and molecular evolution of key viral genes, such as nucleoprotein (N) gene. Based on public data, measles epidemiological information and MeV N gene sequences reported in Shandong Province, China were comprehensively collected and systematically analyzed. The results showed a positive correlation between population density and measles incidence (r = +0.31), while negative correlations were found between measles incidence and healthcare condition (r = -0.21) as well as average routine vaccination rate (r = -0.11). Additionally, the predominant lineage of MeV in Shandong was formed by genotype H1 strains, and the time of the most recent common ancestor of the N gene of MeV genotype H1 in Shandong traced back to 1987 (95% highest posterior density, 1984-1990) with relatively rapid evolution (mean rate, 1.267 × 10-3 substitutions/site/year). The genetic diversity of MeV N gene increased with the substantial emergence of major divergent clades of genotype H1 before 2005 and then remained relatively high and stable. In summary, these findings provided a significant insight into the measles elimination.

Measles disease outbreak and genotype identification in Libya, 2018

Background: There is no data published related to measles outbreaks in Libya. The study aims to report a descriptive analysis of measles outbreaks that occurred in 2018. Methods: Retrospective data of measles outbreaks in 2018 were analysed to describe the characteristics of the outbreaks and their incidence in Libya. Data aggregations of seven outbreaks were extracted during the period January to December 2018 from the National Measles Surveillance Programme which is the official institute responsible for measles surveillance in the country. Data were categorised as confirmed measles cases, district distribution, deaths, age distribution, sex ratio, monthly trends, and measles vaccination status in the outbreaks. Also, the measles virus genotype was identified and compared with the reference strain. Results: A total of 934 confirmed measles cases were detected in seven outbreaks in different locations of the country in 2018. The biggest outbreak was found in Zliten (449 measles cases, 48.0%) followed by Benghazi (374 measles cases, 40.0%). The majority were below 15 years (811 measles cases, 87.0%). The incidence rate of cases was 223/million population. The peak of occurrence began in June 2018 and continued to December. Children with measles who had completed two doses of vaccines were 18.0%, whilst 62.0% were unvaccinated. The genotype sequence was identified in three outbreaks being B3. Conclusion: A significant measles incidence was detected in many outbreaks mainly in the age group below 15 years. The immunity building programme must be evaluated to address the weakness of routine immunisation.

Molecular identification and characterization of measles virus genotypes circulating in Afghanistan, 2008-2018.

The measles virus (MV) remains a leading cause of morbidity and mortality in children under 5 years of age. Molecular identification of circulating wild-type MV) strains is a vital component of the measles elimination program. We received 159 oral swab samples from Afghanistan during 2008-2018. Viral RNA was extracted, followed by one-step RT-PCR and positive amplicons were subject to sequencing for genotype identification. Out of 159 total samples, 52% (83/159) were detected positive by RT-PCR. Genotype D4 was identified from 2.4% (2/83), genotype H1, 4.8% (4/83),and genotype B3, 92.7% (77/83) cases, respectively.

Епідемічні реалії кору на Тернопільщині

Кір є інфекцією, керованою засобами вакцинації, що продовжує залишатись величезною соціально-економічною проблемою для Тернопільщини. У роботі проаналізовано матеріали звітної документації Головного управління Держсанепідслужби та дитячих інфекційних стаціонарів у Тернопільській області. Захворюваність на кір, що фіксувалася за час незалежності країни, значно перевищувала загальноукраїнські показники, зберігала типову для довакцинального періоду періодичність епідемологічних підйомів. В усі проаналізовані пікові періоди діти шкільного віку були найбільш вразливою щодо кору віковою категорією. Виявлено стійку тенденцію до зміщення захворюваності на старший шкільний вік та в бік дорослого населення. Серед захворілих фіксувався високий відсоток щеплених. Лабораторно підтверджено появу вірусу кору генотипу D4 під час останнього спалаху захворювання в області. Аналіз спалахів кору відображає потребу у поглибленні вивчення особливостей становлення поствакцинального протикорового імунітету в сучасних умовах з урахуванням потреби в дослідженні певних імунологічних феноменів.

Epidemiological and Molecular-Genetic Characteristics of the Measles Outbreak in Kazakhstan

Introduction: Genetic characterization of measles viruses (MVs) is an important component of laboratory surveillance of measles. In this study, a phylogenetic analysis was performed of the nucleoprotein gene sequences isolated in the Republic of Kazakhstan in 2018 year. Objective: To study the epidemiological characteristics of measles and identify the circulating strain in the Republic of Kazakhstan during the period of increasing incidence for 36 global efforts to eliminate measles among the population. Material and Methods: On the basis of the reference laboratory “Center for Sanitary and Epidemiological Expertise and Monitoring” of the RSE at the PEM “NCPH” genotyping of measles virus isolated from biological material (urine) from laboratory-confirmed cases was performed. Results: According to the results of the study, it was revealed that the genotypes of the measles virus circulating in the Republic of Kazakhstan belong to two genotypes, the majority of samples (n=16) belonged to the D8genotype and2 samplesto the B3 genotype/MVi/Harare.ZWE/38.09./.

Measles and rubella in the North-West of Russia in period of elimination

Aim: To evaluate the epidemic situation on measles and rubella and to carry out the laboratory diagnostics of these infections in the North-West of Russia in the period of elimination.Materials and Methods. In 2016-2019 a total of 534 blood serum samples from patients with measles diagnosis, 210 – from patients with rubella diagnosis and 1251 – from patients with exanthema were studied by ELISA using “VectoMeasles-IgM” and “EIA-Rubella-IgM” test-systems.Results. Measles incidence in NWR varied from 0 to 0.96 per 100,000 in 2016 and 2019, respectively. Among measles patients the proportion of children and adults changed in 2018-2019, adults constituted 65.9%. Patients not vaccinated against measles and those with the unknown vaccination status were mainly involved in epidemic process (85%). High level of patients with revaccination status was revealed in 2018 (18.4%). These patients demonstrated high levels of IgG (&gt;3.0 IU/ml) as well as high percentage of IgG avidity (&gt;94.3%) on 4-7th day of rash onset thus evidencing secondary immune response. Molecular studies of the samples from patients revealed the circulation of D8 and B3 genotypes of measles virus. Strains of D8 and B3 genotypes were represented by 3 and 4 variants, respectively. Rubella incidence did not exceed 0.13 per 100,000. Strains of rubella virus of genotype 1E were detected.Conclusion. The data of annual measles incidence and molecular studies of circulating wild type measles viruses prove the on-going measles elimination process in the NorthWest of Russia. For rubella, the persistent phase of elimination was demonstrated in the region.

Survey of SARS-CoV-2 genetic diversity in two major Brazilian cities using a fast and affordable Sanger sequencing strategy

Genetic variants of SARS-CoV-2 have been emerging and circulating in many places across the world. Rapid detection of these variants is essential since their dissemination can impact transmission rates, diagnostic procedures, disease severity, response to vaccines or patient management. Sanger sequencing has been used as the preferred approach for variant detection among circulating human immunodeficiency and measles virus genotypes. Using primers to amplify a fragment of the SARS-CoV-2 genome encoding part of the Spike protein, we showed that Sanger sequencing allowed us to rapidly detect the introduction and spread of three distinct SARS-CoV-2 variants in two major Brazilian cities. In both cities, after the predominance of variants closely related to the virus first identified in China, the emergence of the P.2 variant was quickly followed by the detection of the P1 variant, which became dominant in less than one month after it was first detected.

Genetic Characterizations and Molecular Evolution of the Measles Virus Genotype B3's Hemagglutinin (H) Gene in the Elimination Era.

Measles virus (MeV) genotype B3 is one globally significant circulating genotype. Here, we present a systematic description of long-term evolutionary characterizations of the MeV genotype B3’s hemagglutinin (H) gene in the elimination era. Our results show that the B3 H gene can be divided into two main sub-genotypes, and the highest intra-genotypic diversity was observed in 2004. MeV genotype B3’s H gene diverged in 1976; its overall nucleotide substitution rate is estimated to be 5.697 × 10−4 substitutions/site/year, and is slowing down. The amino acid substitution rate of genotype B3’s H gene is also decreasing, and the mean effective population size has been in a downward trend since 2000. Selection pressure analysis only recognized a few sites under positive selection, and the number of positive selection sites is getting smaller. All of these observations may reveal that genotype B3’s H gene is not under strong selection pressure, and is becoming increasingly conservative. MeV H-gene or whole-genome sequencing should be routine, so as to better elucidate the molecular epidemiology of MeV in the future.

Surveillance and genetic characteristics of imported cases of measles virus of D8 genotype in Hebei province

Objective: To understand the epidemiological and genotypic characteristics of imported cases of measles virus of D8 genotype in Hebei province. Methods: Epidemiological investigation of measles cases in surveillance was carried out. The throat swabs of the measles cases in acute phase were collected for real time RT-PCR identification, measles virus culture and genotype identification. Results: A total of 36 imported measles cases of genotype D8 were detected. The cases were mainly distributed in 8 counties of Handan city. Number of confirmed measles cases in Cheng'an county was the highest, accounting for 58.33% (21/36) of all the reported cases. All patients had fever and rash, and 55.55% (20/36) of the cases were under 2 years old and 86.11% (31/36) of the cases had no immunization history. The children with pneumonia accounted for 44.12% (15/34) of the total children with D8 genotype measles virus infection. The nucleotide and amino acid homologies between the imported measles virus genotype D8 and the WHO reference strain of D8 genotype (D8-Manchester.UNK/30.94) were 98.4%-98.6% and 97.3%, respectively. Compared with the strains of H1 genotype in China, the nucleotide and amino acid homologies were 92.8%-93.1% and 93.3%, respectively. Conclusions: The imported cases of measles virus of D8 genotype might have caused local transmission in Hebei province. Molecular epidemiological surveillance for measles virus needs to be further strengthened. It is necessary to detect and control the epidemic early and improve the coverage rate and timely rate of measles vaccination. It is also important to prevent cross infection in hospitals.

Serotypic evolution of measles virus is constrained by multiple co-dominant B cell epitopes on its surface glycoproteins

SummaryAfter centuries of pestilence and decades of global vaccination, measles virus (MeV) genotypes capable of evading vaccine-induced immunity have not emerged. Here, by systematically building mutations into the hemagglutinin (H) glycoprotein of an attenuated measles virus strain and assaying for serum neutralization, we show that virus evolution is severely constrained by the existence of numerous co-dominant H glycoprotein antigenic sites, some critical for binding to the pathogenicity receptors SLAMF1 and nectin-4. We further demonstrate the existence in serum of protective neutralizing antibodies targeting co-dominant fusion (F) glycoprotein epitopes. Lack of a substantial reduction in serum neutralization of mutant measles viruses that retain even one of the co-dominant antigenic sites makes evolution of pathogenic measles viruses capable of escaping serum neutralization in vaccinated individuals extremely unlikely.

An efficient molecular approach to distinguish chains of measles virus transmission in the elimination phase.

Measles viruses continue to spread globally, despite the availability of a safe and effective vaccine. Molecular surveillance of measles virus has become an essential tool to demonstrate whether cascades of infections in a certain region or country are the result of endemic spread or the repeatedly introduction of the virus in contained outbreaks. Currently, molecular surveillance of measles viruses worldwide is mainly based on 450 nucleotides of the C-terminal region of the nucleoprotein (N450). However, as a result of the disappearance of particular measles virus clades over the past decades, this gene segment does not provide sufficient resolution anymore to answer these questions. To increase the molecular resolution, sequence data were collected from three regions of the measles virus genome, the partial non-coding region between the M and F gene (M-F NCR4465-4754), partial H gene (H8022-8621) and the partial L gene (L10724-11438) for measles viruses detected in 2018 and 2019 in the Netherlands. Analysis of obtained sequence data indicated that sequencing of these three regions resulted in an increase in molecular resolution for measles virus genotype B3 and D8 viruses, two of the four global genotypes currently predominant in the European region. Furthermore, this improved resolution was sufficient to support an epidemiology characterized by repeat introduction of measles virus rather than endemic virus spread. In conclusion, sequencing of the M-F NCR4465-4754, H8022-8621 and L10724-11438 regions of the measles virus is an efficient and useful approach for molecular surveillance of measles viruses.

Evaluation of a measles virus multiplex, triple-target real-time RT-PCR in three specimen matrices at a U.S. academic medical center.

Measles virus (MeV) is an important cause of acute febrile illness and pediatric mortality globally, with recent U.S. outbreaks associated with under-vaccination. MeV is highly contagious and timely diagnosis is critical to limit spread. RNA detection is the most sensitive method for acute measles diagnosis; however, MeV nucleic acid amplification assays are not widely available. We performed a diagnostic accuracy study of a triple-target, real-time RT-PCR (rRT-PCR) assay for simultaneous detection of MeV N, H, and L genes. The MeV triple-target rRT-PCR was tested against serial dilutions (7.0-2.0 log10 copies/mL) of five MeV isolates representing circulating genotypes, and detected 98.7% (74/75) of nasopharyngeal (NP) swab dilutions, 100% (75/75) of plasma dilutions, and 85.3% (64/75) of urine dilutions. MeV RNA detection in urine was markedly improved with the addition of a nucleic acid stabilizing agent. A 95% lower limit of detection (LLOD) of < 3.0 log10 copies/mL was established in each specimen matrix. No cross-reactivity with relevant viruses or interfering substances were identified in specificity studies. The MeV triple-target rRT-PCR detected all three gene targets in a clinical NP swab from an individual with confirmed measles infection. Furthermore, pooled testing from 798 influenza A/B/RSV-negative pediatric NP swabs identified two specimens positive for MeV RNA, confirmed by N gene sequencing to represent shedding of the vaccine-type measles virus. The MeV triple-target rRT-PCR assay showed high analytic sensitivity across circulating MeV genotypes in three clinically-relevant matrices. Implementation of this assay in the clinical laboratory may facilitate timely diagnosis of acute measles infection and implementation of appropriate infection control interventions.

Rise in 2017-2018 measles morbidity in Serbia and Northwest Russia

In 2017, the WHO registered 23,927 measles cases in 44 out of 53 countries in the European region. In 2018, measles incidence rate increased up to 82,599 cases registered in 48 countries of the region, with a large number of measles-associated deaths. Overall, 72 measles fatalities were registered in 10 European countries, including Serbia (15 cases).Aim of the study: to characterize 2017—2018 epidemiological upsurge of measles incidence rate observed in the Republic of Serbia (RS) and the Northwestern Federal District (NWFD) of the Russian Federation.Materials and methods. During the 2017—2018 season, 944 serum samples were collected from patients with measles, rubella, or exanthematous diseases in the NWFD and tested in the Laboratory of Virology at the St. Petersburg Regional Centre for Measles Surveillance (SPbRC). In 2017—2018, 2,946 serum samples from the Republic of Serbia were analyzed in the SPbRC by using ELISA with IgM measles test system (Vector-Best, Russia; or Siemens, Germany). Urine and swab samples were examined by RT-PCR and used for isolation and genotyping of measles viruses.Results. From 2017 to 2018, 5,798 measles cases were registered in the RS, among which 2,946 were laboratory-confirmed (serological testing and/or PCR). Unvaccinated subjects or those with unknown vaccination status accounted for majority of the cases. Children under 5 years of age and adults aged 30 years and over dominated among measles patients. During this season, 15 deaths were reported. Several genotypes of measles virus circulated in the RS, e.g. В3 Dublin, D8 Gir Somnath, and D8 Herborn. In 2018, 109 measles cases were recorded in the NWFD, 5 of which were imported from abroad. Among patients, adults comprised 64.2%, wherein 74.3% were covered by unvaccinated subjects or those with unknown vaccination status. Rise in measles incidence rate linked to multiple importations of various measles virus genotypes: В3 Kabul; B3 Dublin; D8 Frankfurt; D8 Cambridge; and D8 Gir Somnath.