Evolutionary genetics of genotype H1 measles viruses in China from 1993 to 2012

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 stable. In summary, these findings provided a significant insight into the measles elimination. This article is protected by copyright. All rights reserved.

Comparative study on molecular epidemiology of measles H1 outbreak and sporadic cases in Shandong Province, 2013–2019

Background

Measles caused by measles virus (MeV) is a highly contagious viral disease which has also been associated with complications including pneumonia, myocarditis, encephalitis, and subacute sclerosing panencephalitis. The current study isolated 33 strains belonging to 2 groups, outbreak and sporadic strains, in 13 cities of Shandong province, China from 2013 to 2019. Comparison of genetic characterization among 15 outbreak strains and 18 sporadic strains was performed by analyzing nucleotide sequences of the C-terminal region of N protein gene (N-450).

Results

All 33 stains belonged to genotype H1. The outbreak strains and sporadic strains distributed crossly in phylogenetic tree. Sequences alignment revealed some interesting G to A transversion which changed the amino acids on genomic sites 1317, 1422, and 1543. The nucleotide and amino acid similarities among outbreak isolates were 98–100% (0–10 nucleotide variations) and 97.7–100%, respectively; They were 97.3–100% and 96.6–100%, respectively for sporadic isolates. Evolutionary genetics analysis revealed that the mean evolution rates of outbreak and sporadic isolates were 1.26 N 10− 3 and 1.48 N 10− 3 substitutions per site per year separately, which were similar with corresponding data before 2012. Local transmission analysis suggested that there were three transmission chains in this study, two of them originated from Japan. Outbreak cases and sporadic cases emerged alternatively and were reciprocal causation on the transmission chains.

Conclusions

Our study investigated the phylogeny and evolutional genetics of MeV during a 7-year surveillance, and compared epidemic and genetic characteristics of outbreak strains and sporadic strains. These results underscore the importance of evolutionary study alongside with sporadic cases in discovering and tracing possible outbreaks, especially in the stage of measles elimination.

Molecular evolution and genomic characteristics of genotype H1 of measles virus

Measles is one of the most infectious diseases of humans. It is caused by the measles virus (MeV) and can lead to serious illness, lifelong complications, and even death. Whole-genome sequencing (WGS) is now available to study molecular epidemiology and identify MeV transmission pathways. In the present study, WGS of 23 MeV strains of genotype H1, collected in Mainland China between 2006 and 2018, were generated and compared to 31 WGSs from the public domain to analyze genomic characteristics, evolutionary rates and date of emergence of H1 genotype. The noncoding region between M and F protein genes (M/F NCR) was the most variable region throughout the genome. Although the nucleotide substitution rate of H1 WGS was around 0.75 × 10^-3 substitution per site per year, the M/F NCR had an evolutionary rate three times higher, with 2.44 × 10^-3 substitution per site per year. Phylogenetic analysis identified three distinct genetic groups. The Time of the Most Recent Common Ancestor (TMRCA) of H1 genotype was estimated at approximately 1988, while the first genetic group appeared around 1995 followed by two other genetic groups in 1999-2002. Bayesian skyline plot showed that the genetic diversity of the H1 genotype remained stable even though the number of MeV cases decreased 50 times between 2014 (52 628) and 2020 (993). The current coronavirus disease 2019 (COVID-19) pandemic might have some effect on the measles epidemic and further studies will be necessary to assess the genetic diversity of the H1 genotype in a post-COVID area.

The genotype distribution and phylodynamic of measles viruses circulating in the east of China in postvaccine era, 2005-2017

The increase of the evolutionary pressure will cause phylodynamics changes of viruses. In post-vaccine coverage era, measles viruses face more immune pressure than ever before. Vice versa, the phylodynamic changes may reflect herd immunity level provided by vaccination. In this study, we analyzed phylodynamic characteristics of measles viruses isolated from 2005 to 2017 in Jiangsu province of China using nucleoprotein gene sequences of measles viruses. The phylogenetic tree was constructed with Markov chain Monte Carlo algorithm. The mean gene distance within each group was computed with MEGA7.0 software. Our results showed that a decline trend is observed in the gene distance of nucleoprotein gene with time as well as incidence of measles from epidemic surveillance system. Two clusters of H1a genotype show cocirculation of multiple variants in early years and the disappearance of most variants with time. We explore the phylodynamic of measles virus under high immune pressure. Our findings highlight that phylodynamic of measles viruses is a helpful tool to assess the effectiveness of epidemic control.

Epidemiological Investigation and Virus Tracing of a Measles Outbreak in Zhoushan Islands, China, 2019

Background: Measles transmissions due to case importations challenge public health systems globally and herd immunities in all countries. In 2019, an imported measles case and its subsequently outbreak was found in the Zhoushan Islands. Here, the process of epidemiological investigation and virus tracing were summarized to provide references for the prevention and control of measles in the future. Materials and methods: The data on the demographic, epidemiological, and clinical manifestation of measles cases in this outbreak were collected. The 450 bp fragments of the measles virus (MeV) N gene were amplified and sequenced. The genome of the first imported case was further isolated. Then, the maximum-likelihood and time-scaled phylogenetic analysis was conducted. Results: A total of 28 measles cases were confirmed. Their onsets were between March 13 and May 18, 2019. The first patient was from the Ukraine. He was confirmed at the Fever Clinic in Zhoushan hospital on March 15, 2019 and at the same time, another patient had visited the hospital due to another illness and 10 days later, this second case had onset (March 25, 2019). The epidemic curve shows sustained community transmission. The majority of the following cases (19/26) were clustered on the Donggang street which was close to where the second case worked. The 22 measles virus strains successfully isolated from this outbreak all belonged to the D8.2a sub-cluster and clustered with the KY120864/MVs/GirSomnath.IND/42.16/[D8] which was the predominant genotype in the Ukraine during 2018-2019. The analysis of the complete D8 genotype genome pointed to the fact that this prevailing strain originated from India in 2015 and its substitution rate was estimated as 6.91 × 10^-4 (5.64-7.98 × 10^-4) nucleotide substitutions/site/year. Conclusion: This outbreak was caused by an imported case from the Ukraine. There was a possible nosocomial infection between the first case and the second case. Then, the second case played an important role in the spread of virus due to her occupation. The molecular phylogenetic analysis could help to track the origin of the virus. Increasing and maintaining the high level of vaccination coverage (≥95%) and an efficient response to imported cases are essential to prevent and control the recurrence and outbreak of measles virus.

Phylogenetic and Epidemiological Analysis of Measles Viruses in Shenzhen, China from January 2015 to July 2019

Background

Measles morbidity and mortality were significantly reduced after the measles vaccine was introduced in China in 1965. However, measles outbreaks easily occur in densely populated areas, especially where there is no universal vaccination. The outbreak that occurred in Shenzhen, the Chinese city with the largest internal immigration, provides a lesson in measles virus mutation and measles prevention. The present study is a phylogenetic analysis of measles viruses and comparison of clinical signs between individuals with and without vaccination.

Material/Methods

We performed phylogenetic analysis of the nucleoprotein (N) genes of measles virus from 129 measles patients in Shenzhen from January 2015 to July 2019. Phylogenetic trees were constructed using the neighbor-joining method.

Results

The phylogenetic analysis showed all viruses were classified into genotype H1. In addition, there is often a seasonal measles outbreak in July each year. The clinical data showed that patients who were unvaccinated were more likely to have coughing, chronic bronchitis, conjunctivitis, catarrh, Koplik spots, and diarrhea. Children of migrant workers and those living in mountainous and rural districts accounted for most measles cases.

Conclusions

Our results showed there was a seasonal measles outbreak in Shenzhen Children’s Hospital. All the measles virus from 129 measles patients were H1 viruses. The clinical signs also showed a difference between unvaccinated and vaccinated patients. Moreover, most of the unvaccinated patients came from migrant worker families. We suggest there is a need for increased health promotion and vaccination programs for migrant workers and people living in remote villages.

Nationwide Molecular Epidemiology of Measles Virus in Japan Between 2008 and 2017

Genotyping evidence that supports the interruption of endemic measles virus (MV) transmission is one of the essential criteria to be verified in achieving measles elimination. In Japan since 2014, MV genotype analyses have been performed for most of the measles cases in prefectural public health institutes nationwide. With this strong molecular epidemiological data, Japan was verified to have eliminated measles in March, 2015. However, even in the postelimination era, sporadic cases and small outbreaks of measles have been detected repeatedly in Japan. This study investigated the nationwide molecular epidemiology of MV between 2008 and 2017. The 891 strains in the total period between 2008 and 2017 belonged to seven genotypes (D5, D4, D9, H1, G3, B3, and D8) and 124 different MV sequence variants, based on the 450-nucleotide sequence region of the N gene (N450). The 311 MV strains in the postelimination era between 2015 and 2017 were classified into 1, 7, 8, and 32 different N450 sequence variants in D9, H1, B3, and D8 genotypes, respectively. Analysis of the detection period of the individual N450 sequence variants showed that the majority of MV strains were detected only for a short period. However, MV strains, MVs/Osaka.JPN/29.15/ [D8] and MVi/Hulu Langat.MYS/26.11/ [D8], which are named strains designated by World Health Organization (WHO), have been detected in many cases over 2 or 3 years between 2015 and 2017. The WHO-named strains have circulated worldwide, causing outbreaks in many countries. Epidemiological investigation revealed repeated importation of these WHO-named strains into Japan. To demonstrate the elimination status (interruption of endemic transmission) in situations with repeated importation of the same strains is challenging. Nevertheless, the detailed sequence analysis of individual MV strains and chronological analysis of these strains provided sufficient evidence to show that Japan has still maintained its measles elimination status in 2017.

Genetic variability of the measles virus hemagglutinin gene in B3 genotype strains circulating in Northern Italy

Sequencing the whole measles virus hemagglutinin (H) gene, in conjunction with a 450-nucleotide region of the nucleoprotein gene (N-450), is helpful for the identification of new genotypes and as an auxiliary in outbreak characterization. In addition, it is essential to be able to predict the antigenic changes of the H protein to gain a better monitoring of the response to the vaccine. In this study, we obtained the full-length H gene sequences from 19 measles virus (MV) strains belonging to two B3 genotype variants circulating in Lombardy (Northern Italy) between July 2015 and February 2016 and evaluated the variability of the whole MV-H gene. Furthermore, we compared the obtained H amino acid sequences to all MV sequences available in the GenBank database (n = 1152 in total) and analyzed the amino acid substitutions in the H protein within clades where the Italian strains were included. We identified a higher variability in the H gene compared to the N-450 region and our results support previous studies, highlighting that the H gene is more informative for characterizing the MV B3 genotype than the N-450 sequence. Some of the amino acid substitutions were fixed in the viral population and, remarkably, some of the amino acid substitutions were typically present only in the Italian sequences. Accumulating further molecular information about MV-H gene will be necessary to enable in-depth analyses of the variability of this gene in the vaccinated population.

Phylogenomic insights to the origin and spread of phocine distemper virus in European harbour seals in 1988 and 2002

The 1988 and 2002 phocine distemper virus (PDV) outbreaks in European harbour seals Phoca vitulina are among the largest mass mortality events recorded in marine mammals. Despite its large impact on harbour seal population numbers, and 3 decades of studies, many questions regarding the spread and temporal origin of PDV remain unanswered. Here, we sequenced and analysed 7123 bp of the PDV genome, including the coding and non-coding regions of the entire P, M, F and H genes in tissues from 44 harbour seals to shed new light on the origin and spread of PDV in 1988 and 2002. The phylogenetic analyses trace the origin of the PDV strain causing the 1988 outbreak to between May 1987 and April 1988, while the origin of the strain causing the 2002 outbreak can be traced back to between June 2001 and May 2002. The analyses further point to several independent introductions of PDV in 1988, possibly linked to a southward mass immigration of harp seals in the winter and spring of 1987-1988. The vector for the 2002 outbreak is unknown, but the epidemiological analyses suggest the subsequent spread of PDV from the epicentre in the Kattegat, Denmark, to haul-out sites in the North Sea through several independent introductions.

The first outbreak of measles virus caused by imported genotype D8 in Jiangsu province of China

Here we reported the outbreak of measles cases caused by the genotype D8 measles virus for the first time in Jiangsu province in China, which was possibly imported by a foreign student from Laos. Throat swab specimens were collected, and used to isolate virus. 634-bp fragment of the N gene and 1854-bp fragment of H gene were amplified by reverse transcription-PCR and sequenced, respectively. Phylogenetic results indicated that they belonged to genotype D8 measles virus. Further epidemiology investigation showed that the adults with D8 measles virus infection did not receive measles vaccine before having measles. In China, almost all D8 genotype MeV only infected those population without receiving measles vaccine immunization. Therefore, it is still necessary to implement the supplement activity of measles immunization target adult with immunity gap.

Importance of real-time RT-PCR to supplement the laboratory diagnosis in the measles elimination program in China

In addition to high vaccination coverage, timely and accurate laboratory confirmation of measles cases is critical to interrupt measles transmission. To evaluate the role of real-time reverse transcription-polymerase chain reaction (RT-PCR) in the diagnosis of measles cases, 46,363 suspected measles cases with rash and 395 suspected measles cases without rash were analyzed in this study; the cases were obtained from the Chinese measles surveillance system (MSS) during 2014–2017 and simultaneously detected by measles-specific IgM enzyme-linked immunosorbent assay (ELISA) and real-time RT-PCR. However, some IgM-negative measles cases were identified by real-time RT-PCR. The proportion of these IgM-negative and viral nucleic acid-positive measles cases was high among measles cases with measles vaccination history, cases without rash symptoms, and cases within 3 days of specimen collection after onset. The proportion of IgM-negative and viral nucleic acid-positive measles cases in the 0–3 day group was up to 14.4% for measles cases with rash and 40% for measles cases without rash. Moreover, the proportions of IgM-negative and nucleic acid-positive measles cases gradually increased with the increase in the measles vaccination dose. Therefore, integrated with IgM ELISA, real-time RT-PCR would greatly improve the accurate diagnosis of measles cases and avoid missing the measles cases, especially for measles cases during the first few days after onset when the patients were highly contagious and for measles cases with secondary vaccine failure. In conclusion, our study reconfirmed that IgM ELISA is the gold-standard detection assay for measles cases confirmation. However, real-time RT-PCR should be introduced and used to supplement the laboratory diagnosis, especially in the setting of pre-elimination and/or elimination wherever appropriate.

The importance of serological and molecular analyses for the diagnosis of measles cases and for meeting elimination targets in Turkey from 2007 to 2015

Measles is an important childhood infection targeted to be eliminated by the World Health Organization (WHO). Virus circulation has not been interrupted in the European Region because high vaccination rates could not be achieved among some countries of the WHO European Region including Turkey. The purpose of this study was to evaluate the laboratory findings of measles cases confirmed in the last nine years, to assess the epidemiological data of the cases, to determine the molecular genotyping studies and to emphasise the importance of laboratory-based surveillance in measles. From 2007 to 2010, only 18 imported cases were detected in Turkey. However, this number increased with a local outbreak of 111 cases in 2011, followed by another outbreak in 2012 in Istanbul that spread countrywide in the following two years; a total of 8661 laboratory-confirmed measles cases were reported from 2012 to 2015. After ELISA detection of a measles IgM-positive result in serum samples of potential measles cases, RT-PCR was performed with urine or nasopharyngeal swab samples of patients, and amplicons were subjected to sequencing. In the samples of 2010 and 2011, D4 and D9 genotypes were mainly detected; as of 2012, the D8 genotype has gained importance. Although D8 was also identified in 2014, in the same year genotype H1 viruses were detected in Turkey for the first time. Therefore, it is important to perform a genotypic analysis of the virus causing the outbreak, analyse epidemiological connections of the contact, determine the source of the outbreak and plan measures based on this information.

Evolutionary analysis of mumps viruses of genotype F collected in mainland China in 2001-2015

Mumps incidence in mainland China remains at a high level. Genotype F has been the predominant genotype of mumps virus (MuV) in the last 20 years in mainland China. To better understand the genetic characteristics of MuV in China, the sequences of the Small Hydrophobic (SH), Hemagglutinin-Neuraminidase (HN) and Fusion (F) genes of MuVs of genotype F collected during 2001-2015 were determined. The evolutionary rates of the HN and F genes were similar (0.5 × 10-3 substitutions/site/year) whereas the SH gene evolutionary rate was three times faster. The most recent common ancestor of genotype F was traced back to 1980. Four lineages were identified within HN and F MuV sequences. A phylogeographic analysis indicated that the genotype F viruses originally spread from the Liaoning and Shandong provinces followed by a spread to the South and East of China. This study provides important genetic baseline data for the development of prevention and control measures of mumps.

Global and national laboratory networks support high quality surveillance for measles and rubella

Laboratory networks are an essential component of disease surveillance systems because they provide accurate and timely confirmation of infection. WHO coordinates global laboratory surveillance of vaccine preventable diseases, including measles and rubella. The more than 700 laboratories within the WHO Global Measles and Rubella Laboratory Network (GMRLN) supports surveillance for measles, rubella and congenial rubella syndrome in 191 counties. This paper describes the overall structure and function of the GMRLN and highlights the largest of the national laboratory networks, the China Measles and Rubella Laboratory Network.

Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique

Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples. Human rhinovirus C was the virus most frequently detected and was identified in seven samples. Human measles virus, adenovirus B 55 and coxsackievirus A10 were also identified. Metagenomic sequencing also provided virus genomic sequences, which enabled genotype characterization and phylogenetic analysis. For cases of multiple infection, metagenomic sequencing afforded information regarding the quantity of each virus in the sample, which could be used to evaluate each viruses' role in the disease. Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.

Measles

Measles is an infectious disease in humans caused by the measles virus (MeV). Before the introduction of an effective measles vaccine, virtually everyone experienced measles during childhood. Symptoms of measles include fever and maculopapular skin rash accompanied by cough, coryza and/or conjunctivitis. MeV causes immunosuppression, and severe sequelae of measles include pneumonia, gastroenteritis, blindness, measles inclusion body encephalitis and subacute sclerosing panencephalitis. Case confirmation depends on clinical presentation and results of laboratory tests, including the detection of anti-MeV IgM antibodies and/or viral RNA. All current measles vaccines contain a live attenuated strain of MeV, and great progress has been made to increase global vaccination coverage to drive down the incidence of measles. However, endemic transmission continues in many parts of the world. Measles remains a considerable cause of childhood mortality worldwide, with estimates that >100,000 fatal cases occur each year. Case fatality ratio estimates vary from <0.01% in industrialized countries to >5% in developing countries. All six WHO regions have set goals to eliminate endemic transmission of MeV by achieving and maintaining high levels of vaccination coverage accompanied by a sensitive surveillance system. Because of the availability of a highly effective and relatively inexpensive vaccine, the monotypic nature of the virus and the lack of an animal reservoir, measles is considered a candidate for eradication.

PACT- and RIG-I-Dependent Activation of Type I Interferon Production by a Defective Interfering RNA Derived from Measles Virus Vaccine

The live attenuated measles virus vaccine is highly immunostimulatory. Identification and characterization of its components that activate the innate immune response might provide new strategies and agents for the rational design and development of chemically defined adjuvants. In this study, we report on the activation of type I interferon (IFN) production by a defective interfering (DI) RNA isolated from the Hu-191 vaccine strain of measles virus. We found that the Hu-191 virus induced IFN-β much more potently than the Edmonston strain. In the search for IFN-inducing species in Hu-191, we identified a DI RNA specifically expressed by this strain. This DI RNA, which was of the copy-back type, was predicted to fold into a hairpin structure with a long double-stranded stem region of 206 bp, and it potently induced the expression of IFN-β. Its IFN-β-inducing activity was further enhanced when both cytoplasmic RNA sensor RIG-I and its partner, PACT, were overexpressed. On the contrary, this activity was abrogated in cells deficient in PACT or RIG-I. The DI RNA was found to be associated with PACT in infected cells. In addition, both the 5'-di/triphosphate end and the double-stranded stem region on the DI RNA were essential for its activation of PACT and RIG-I. Taken together, our findings support a model in which a viral DI RNA is sensed by PACT and RIG-I to initiate an innate antiviral response. Our work might also provide a foundation for identifying physiological PACT ligands and developing novel adjuvants or antivirals.

IMPORTANCE

The live attenuated measles virus vaccine is one of the most successful human vaccines and has largely contained the devastating impact of a highly contagious virus. Identifying the components in this vaccine that stimulate the host immune response and understanding their mechanism of action might help to design and develop better adjuvants, vaccines, antivirals, and immunotherapeutic agents. We identified and characterized a defective interfering RNA from the Hu-191 vaccine strain of measles virus which has safely been used in millions of people for many years. We further demonstrated that this RNA potently induces an antiviral immune response through cellular sensors of viral RNA known as PACT and RIG-I. Similar types of viral RNA that bind with and activate PACT and RIG-I might retain the immunostimulatory property of measles virus vaccines but would not induce adaptive immunity. They are potentially useful as chemically defined vaccine adjuvants, antivirals, and immunostimulatory agents.

Genetic characterization of measles virus in the Philippines, 2008-2011

Background

Large outbreaks of measles occurred in the Philippines in 2010 and 2011. Genetic analysis was performed to identify the genotype of measles virus (MeV) that was responsible for the large outbreaks.

Methods

A total of 114 representative MeVs that were detected in the Philippines from 2008 to 2011 were analyzed by sequencing the C-terminal region of nucleocapsid (N) gene and partial hemagglutinin (H) gene and by inferring the phylogenetic trees.

Results

Genetic analysis showed that genotype D9 was the predominant circulating strain during the 4-year study period. Genotype D9 was detected in 23 samples (92%) by N gene sequencing and 93 samples (94%) by H gene analysis. Sporadic cases of genotype G3 MeV were identified in 2 samples (8%) by N gene sequencing and 6 samples (6%) by H gene analysis. Genotype G3 MeV was detected mainly in Panay Island in 2009 and 2010. Molecular clock analysis of N gene showed that the recent genotype D9 viruses that caused the big outbreaks in 2010 and 2011 diverged from a common ancestor in 2005 in one of the neighboring Southeast Asian countries, where D9 was endemic. These big outbreaks of measles resulted in a spillover and were associated with genotype D9 MeV importation to Japan and the USA.

Conclusion

Genotype D9 MeV became endemic and caused two big outbreaks in the Philippines in 2010 and 2011. Genotype G3 MeV was detected sporadically with limited geographic distribution. This study highlights the importance of genetic analysis not only in helping with the assessment of measles elimination program in the country but also in elucidating the transmission dynamics of measles virus.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-015-1201-1) contains supplementary material, which is available to authorized users.

Measles virus genetic evolution throughout an imported epidemic outbreak in a highly vaccinated population

Measles virus circulates endemically in African and Asian large urban populations, causing outbreaks worldwide in populations with up-to-95% immune protection. We studied the natural genetic variability of genotype B3.1 in a population with 95% vaccine coverage throughout an imported six month measles outbreak. From first pass viral isolates of 47 patients we performed direct sequencing of genomic cDNA. Whilst no variation from index case sequence occurred in the Nucleocapsid gene hyper-variable carboxy end, in the Hemagglutinin gene, main target for neutralizing antibodies, we observed gradual nucleotide divergence from index case along the outbreak (0% to 0.380%, average 0.138%) with the emergence of transient and persistent non-synonymous and synonymous mutations. Little or no variation was observed between the index and last outbreak cases in Phosphoprotein, Nucleocapsid, Matrix and Fusion genes. Most of the H non-synonymous mutations were mapped on the protein surface near antigenic and receptors binding sites. We estimated a MV-Hemagglutinin nucleotide substitution rate of 7.28 × 10-6 substitutions/site/day by a Bayesian phylogenetic analysis. The dN/dS analysis did not suggest significant immune or other selective pressures on the H gene during the outbreak. These results emphasize the usefulness of MV-H sequence analysis in measles epidemiological surveillance and elimination programs, and in detection of potentially emergence of measles virus neutralization-resistant mutants.