Molecular epidemiology of measles viruses in China, 1995-2003

Global genetic diversity of measles virus (Paramyxoviridae: Morbillivirus: Morbillivirus hominis): historical aspects and current state

Monitoring the circulation of the measles virus and studying its genetic diversity is an important component of the measles elimination program. A methodological approach to molecular genetic studies and their interpretation in the measles surveillance was developed in the early 2000s. During its development, clear areas of circulation of each genotype of the virus were identified, therefore, the determination of viruses' genotypes was proposed to monitor circulation and identify transmission pathways. However, in the future, due to a significant decrease in the number of active genotypes, an approach based on sub-genotyping was proposed: determining not only the genotype of the virus, but also its genetic lineage/genetic variant. The Global Measles and Rubella Laboratory Network (GMRLN) systematically monitors the circulation of the measles virus at the sub-genotypic level, depositing the results in a specialized database MeaNS2. It is this database that is the most complete and reliable source of information about the genetic characteristic of measles viruses. This review presents both historical information and the latest data on the global genetic diversity of the measles virus.

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.

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.

The Detection and Characterization of Herpes Simplex Virus Type 1 in Confirmed Measles Cases

Based on measles surveillance in Shanghai, People's Republic of China, from 2006 to 2015, we found that measles virus isolates from 40 throat swab samples exhibited atypical cytopathic effects in Vero/hSLAM cells, which was found to be a result of coinfection with measles virus (MeV) and human herpes simplex virus type 1 (HSV-1). Serological and molecular approaches were used to confirm and characterize the coinfections in these patients. Among the 40 measles cases, measles-specific IgM was detected in 37 cases, while measles-specific IgG was detected in 27 cases. HSV-1-specific IgM and IgG were detected in 7 and 34 cases, respectively, suggesting that most of the MeV infections were primary, but that HSV-1 infection was due to the reactivation of latent virus in most cases. The titers of HSV-1 IgG in patients with either measles or measles-HSV-1 coinfection were significantly higher than those in the healthy group (P = 0.0026 and P < 0.0001, respectively); however, there was no significant difference in the titers of HSV-1 IgG in the MeV and MeV-HSV-1 coinfection patients (P = 0.105). Nucleic acids from MeV and HSV-1 were detected in 40 and 39 throat swabs, respectively. Twenty five MeV RNA sequences were genotyped, and all represented genotype H1, which is the endemic genotype in China. Sequences from the glycoprotein G gene of HSV-1 were used to classify the isolates into two distinct phylogenetic groups: 34 belonged to group A and 3 belonged to group B.

Molecular characterization of measles viruses in China: Circulation dynamics of the endemic H1 genotype from 2011 to 2017

Due to the Expanded Program on Immunization (EPI) and supplementary immunization activities (SIAs) in China, the incidence of measles in China has decreased extensively. The incidence reached its lowest levels in contemporary history in 2012 and 2017, with incidence rates of 4.6 and 4.3 per million population, respectively. However, more than 147,000 measles cases were reported from 2013 to 2016. Furthermore, the proportions of cases in infants < 8 months and adults have been increasing since 2013, representing a considerable challenge for measles elimination in China. A total of 14,868 measles viruses were isolated from confirmed measles cases from 2011 to 2017, of which 14,631 were identified as the predominant endemic genotype, H1; 87 were identified as genotype A viruses that were vaccine associated strains; and 150 were identified as non-H1 genotype viruses. The non-H1 genotype viruses included 62 D8 viruses, 70 D9 viruses, 3 D11 viruses, 14 B3 viruses, and 1 G3 virus, which were identified as imported or import-related viruses that caused sporadic cases or small outbreaks. Most of the transmission chains detected during the period 2011–2012 were interrupted and were followed by many new transmission chains of unknown origin that spread, causing a large measles resurgence in China during 2013–2016. After 4 years of measles resurgence and continuous implementation of the routine immunization program and SIAs, the population immunity reached a sufficiently high level to interrupt most of the transmission chains; only a few strains survived, which continued to be sporadically detected in China in 2017. In the present study, the results from the combined epidemiological and molecular virological data demonstrated the great progress towards measles elimination in China by the further analysis of circulation dynamics for the endemic H1 genotype measles virus from 2011 to 2017. And this study accumulated critical baseline data on circulating wild-type measles viruses in China and provides comprehensive information to the world. These comprehensive baseline data provide evidence to support measles elimination in the future, not only in China but also in other countries worldwide. In addition, the information will be very useful to other countries for tracing their sources of measles cases and for identifying transmission links, which can help prevent potential measles outbreaks.

The emerging sub-genotype C2 of CoxsackievirusA10 Associated with Hand, Foot and Mouth Disease extensively circulating in mainland of China

Coxsackievirus A10 (CV-A10) associated with Hand, foot, and mouth disease (HFMD) cases emerged increasingly in recent years. In this study, the samples from nation-wide HFMD surveillance, including 27 out of 31 provinces in China were investigated, and the continuous and extensive virological surveillance, covered 13 years, were conducted to provide a comprehensive molecular characterization analysis of CV-A10. 855 CV-A10 viruses (33 severe cases included), were isolated from HFMD children patients during 2009 to 2016 in China. 164 representative sequences from these viruses, together with 117 CV-A10 sequences downloaded from GenBank based on entire VP1 were recruited in this study. Two new genotypes (F and G) and two sub-genotypes (C1 and C2) were identified. Among 264 Chinese sequences, 9 of them were genotype B, 8 of them were C1, and the other (247) were C2, the predominant sub-genotype in China since 2012. Chinese C2 viruses showed obvious temporal characteristics and can be divided into 3 clusters (cluster 1~3). Cluster 3 viruses was circulating extensively during 2014 and 2016 with more severe cases. It is very necessary and important to continuously conduct the extensive virological surveillance for CV-A10, and further evolutionary studies will provide more evidence on its evolution and virulence.

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.

Systematic Review of Measles and Rubella Serology Studies

Serological tests provide information about individual immunity from historical infection or immunization. Cross-sectional serological studies provide data about the age- and sex-specific immunity levels for individuals in the studied population, and these data can provide a point of comparison for the results of transmission models. In the context of developing an integrated model for measles and rubella transmission, we reviewed the existing measles and rubella literature to identify the results of national serological studies that provided cross-sectional estimates of population immunity at the time of data collection. We systematically searched PubMed, the Science Citation Index, and references we identified from relevant articles published in English. We extracted serological data for comparison to transmission model outputs. For rubella, serological studies of women of child-bearing age provide information about the potential risks of infants born with congenital rubella syndrome. Serological studies also document the loss of maternal antibodies, which occurs at different rates for the different viruses and according to the nature of the induced immunity (i.e., infection or vaccine). The serological evidence remains limited for some areas, with studies from developed countries representing a disproportionate part of the evidence. The collection and review of serological evidence can help program managers identify immunity gaps in the population, which may help them better understand the characteristics of individuals within their populations who may participate in transmission and manage risks.

Epidemiological investigation of Measles in Bozhou City, China, from 2005 to 2015

BACKGROUND

Measles is one of the most highly contagious diseases which have not been eliminated in China. This study aimed to investigate the epidemiological characteristics of measles in Bozhou city, China between 2005 and 2015 and provide scientific basis for the prevention, control and elimination of measles.

METHODS

Cases of measles derived from the China Information System for Disease Prevention and Control, and demographic data were obtained from the Public Security Bureau of Bozhou city.

RESULTS

Among the 2934 cases, the average annual incidence of measles was 45.934 (per 1,000,000 persons) and no death occurred. The incidence of males was higher than females (Z = 10.794, p < 0.05). Scattered children accounted for 63.2% (1854/2934) in occupation distributing. In terms of immunization history of cases, 57.5% had 0 doses, 15.0% had one dose, 7.5% had two doses and others were uncertain.

CONCLUSIONS

Our study has investigated the epidemiological characteristics of measles in Bozhou City. To eventually eliminate measles in Bozhou city, improving measles vaccination coverage and quality of routine immunization services were important.

Molecular Characterization of Wild Type Measles Virus from Adult Patients in Northern China, 2014

OBJECTIVES

In this study, we studied the N and H genes from wild type measles viruses (MeVs) isolated during the 2013-2014 outbreak.

METHODS

Clinical samples were collected, and the genotyping, phylogenetic analysis were performed.

RESULTS

The vaccination rate of the study population was 4%. Genotype H1a was the predominant genotype. Wild type viruses were classified into clusters A and B, C and may have different origins. N-450 sequences from wild type viruses were highly homologous with, and likely evolved from MeVs circulating in Tianjing and Henan in 2012. MVs/Shenyang.CHN/18.14/3 could have evolved from MeVs from Liaoning, Beijing, Hebei, Heilongjiang, Henan, Jilin, and Tianjin. Our data suggested that one or more of the same viruses circulated between Beijing, Shenyang, Hong Kong, Taiwan and Berlin.

CONCLUSIONS

Important factors contributing to outbreaks could include weak vaccination coverage, poor vaccination strategies, and migration of adult workers between cities, countries, and from rural areas to urban areas.

Molecular epidemiology of measles virus infection in Shanghai in 2000-2012: the first appearance of genotype D8

Purpose

The purpose of this study was to identify measles virus in Shanghai in 2012 and study the genotype trend of measles virus epidemic strains during 2000–2012.

Methods

Nose and throat swab specimens were collected from 34 suspected measles cases in Shanghai. Measles virus was isolated using Vero-SLAM cells (African green monkey kidney cells/lymphoid signal activating factor-transfected African green monkey kidney cells). The 450 bp of C terminus of the N gene and the entire hemagglutinin gene sequence was amplified using RT-PCR. Phylogenetic analysis was performed by comparing the seven measles strains in Shanghai with the reference strains for H1a, H1b and D8 genotypes, as well as the Chinese measles virus vaccine strain.

Results

Seven measles viruses strains were isolated from the 34 throat swap specimens. Six strains were genotype H1a, which is the predominant strain in China and one strain was genotype D8, which is the first imported strain since 2000. All these seven strains maintained most of the glycosylation sites except subtype H1a, which lost one glycosylation site.

Conclusion

Since 2000, measles virus strains in Shanghai are consistent with measles virus from other provinces in China with H1a being the predominant genotype. This study is also the first report of genotype D8 strain in Shanghai. All strains maintained their glycosylation sites except H1a that lost one glycosylation site. These strains could still be neutralized by the Chinese measles vaccine. We suggest that Shanghai Center for Disease Control laboratories should strengthen their approaches to monitor measles cases to prevent further spread of imported strains.

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

Virologic surveillance is a critical component of measles management. One of the criteria for verification of elimination of endemic measles is genetic analysis of wild-type viruses to demonstrate lack of an indigenous genotype. Measles is yet to be eliminated in China, and genotype H1 has been detected continuously since virologic surveillance was initiated in 1993. Virologic surveillance has been very active in China, providing a unique opportunity to conduct a detailed study of the evolution of a single, endemic genotype over a timespan of nearly two decades. Phylogenetic analysis performed on the 450 nt coding sequence for the C-terminal 150 amino acids of the nucleoprotein (N-450), fusion (F) gene and haemagglutinin (H) gene confirmed the continued circulation of genotype H1 viruses for 19 years. No evidence of selective pressure for the H protein was found. The substitution rates ranged from 0.75×10(-3) substitutions site(-1) year(-1) for H to 1.65×10(-3) substitutions site(-1) year(-1) for N-450. The time of most recent common ancestor (TMRCA) for genotype H1 was estimated as approximately 1985 (95 % highest probability density, 1979-1989). Finally, the overall diversity of measles sequences from China decreased from 2005 to 2012, coincident with a substantial decrease in measles cases. The results suggest that detailed evolutionary analyses should facilitate the documentation of eventual measles elimination in China. Moreover, the molecular approaches used in this study can be applied in other countries approaching measles elimination.

Genetic characterization of the hemagglutinin genes of wild-type measles virus circulating in china, 1993-2009

BACKGROUND

China experienced several large measles outbreaks in the past two decades, and a series of enhanced control measures were implemented to achieve the goal of measles elimination. Molecular epidemiologic surveillance of wild-type measles viruses (MeV) provides valuable information about the viral transmission patterns. Since 1993, virologic surveillnace has confirmed that a single endemic genotype H1 viruses have been predominantly circulating in China. A component of molecular surveillance is to monitor the genetic characteristics of the hemagglutinin (H) gene of MeV, the major target for virus neutralizing antibodies.

PRINCIPAL FINDINGS

Analysis of the sequences of the complete H gene from 56 representative wild-type MeV strains circulating in China during 1993-2009 showed that the H gene sequences were clustered into 2 groups, cluster 1 and cluster 2. Cluster1 strains were the most frequently detected cluster and had a widespread distribution in China after 2000. The predicted amino acid sequences of the H protein were relatively conserved at most of the functionally significant amino acid positions. However, most of the genotype H1 cluster1 viruses had an amino acid substitution (Ser240Asn), which removed a predicted N-linked glycosylation site. In addition, the substitution of Pro397Leu in the hemagglutinin noose epitope (HNE) was identified in 23 of 56 strains. The evolutionary rate of the H gene of the genotype H1 viruses was estimated to be approximately 0.76×10(-3) substitutions per site per year, and the ratio of dN to dS (dN/dS) was <1 indicating the absence of selective pressure.

CONCLUSIONS

Although H genes of the genotype H1 strains were conserved and not subjected to selective pressure, several amino acid substitutions were observed in functionally important positions. Therefore the antigenic and genetic properties of H genes of wild-type MeVs should be monitored as part of routine molecular surveillance for measles in China.

Improving molecular tools for global surveillance of measles virus

BACKGROUND

The genetic characterization of wild-type measles viruses plays an important role in the description of viral transmission pathways and the verification of measles elimination. The 450 nucleotides that encode the carboxyl-terminus of the nucleoprotein (N-450) are routinely sequenced for genotype analysis.

OBJECTIVES

The objectives of this study were to develop improved primers and controls for RT-PCR reactions used for genotyping of measles samples and to develop a method to provide a convenient, safe, and inexpensive means to distribute measles RNA for RT-PCR assays and practice panels.

STUDY DESIGN

A newly designed, genetically defined synthetic RNA and RNA isolated from cells infected with currently circulating genotypes were used to compare the sensitivity of primer pairs in RT-PCR and nested PCR. FTA® cards loaded with lysates of measles infected cells were tested for their ability to preserve viral RNA and destroy virus infectivity.

RESULTS

A new primer pair, MeV216/MeV214, was able to amplify N-450 from viruses representing 10 currently circulating genotypes and a genotype A vaccine strain and demonstrated 100-fold increased sensitivity compared to the previously used primer set. A nested PCR assay further increased the sensitivity of detection from patient samples. A synthetic positive control RNA was developed that produced PCR products that are distinguishable by size from PCR products amplified from clinical samples. FTA® cards completely inactivated measles virus and stabilized RNA for at least six months.

CONCLUSIONS

These improved molecular tools will advance molecular characterization of circulating measles viruses globally and provide enhanced quality control measures.

Molecular characterization of the measles virus genotypes in JiLin Province, China

Measles remains a severe global health threat, and nearly 30 million new cases are reported annually. Although many studies have analyzed measles viruses (MV) at the epidemiologic and phylogenetic levels, no study has yet to integrate these two types of data. To this end, we isolated 16 wild-type MV strains China's Jilin province. The MV genotype H1 was the most prevalent strain. After sequencing the nucleoprotein (N) genes of these strains, a maximum clade credibility tree was constructed by the Bayesian Markov Chain Monte Carlo method using 450 MV strains from GenBank with epidemiological information. The MV N gene evolution rate was 1.127E-3. Analysis of the time of the most recent common ancestor (TMRCA) for genotypes A/B/C/G/H revealed that genotypes D and B had the largest and smallest TMRCA (45.86 and 26.63, respectively). The highest level of genetic diversity for the MV N gene occurred around the year 2000. Here in this study, we uncovered the MV genotypes circulating in China's Jilin Province and estimated the epidemiologic and phylogenetic relationship for the six different genotypes of MV.

Single endemic genotype of measles virus continuously circulating in China for at least 16 years

The incidence of measles in China from 1991 to 2008 was reviewed, and the nucleotide sequences from 1507 measles viruses (MeV) isolated during 1993 to 2008 were phylogenetically analyzed. The results showed that measles epidemics peaked approximately every 3 to 5 years with the range of measles cases detected between 56,850 and 140,048 per year. The Chinese MeV strains represented three genotypes; 1501 H1, 1 H2 and 5 A. Genotype H1 was the predominant genotype throughout China continuously circulating for at least 16 years. Genotype H1 sequences could be divided into two distinct clusters, H1a and H1b. A 4.2% average nucleotide divergence was found between the H1a and H1b clusters, and the nucleotide sequence and predicted amino acid homologies of H1a viruses were 92.3%-100% and 84.7%-100%, H1b were 97.1%-100% and 95.3%-100%, respectively. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Cluster H1a and H1b viruses were co-circulating during 1993 to 2005, while no H1b viruses were detected after 2005 and the transmission of that cluster has presumably been interrupted. Analysis of the nucleotide and predicted amino acid changes in the N proteins of H1a and H1b viruses showed no evidence of selective pressure. This study investigated the genotype and cluster distribution of MeV in China over a 16-year period to establish a genetic baseline before MeV elimination in Western Pacific Region (WPR). Continuous and extensive MeV surveillance and the ability to quickly identify imported cases of measles will become more critical as measles elimination goals are achieved in China in the near future. This is the first report that a single endemic genotype of measles virus has been found to be continuously circulating in one country for at least 16 years.

Trends in notifiable infectious diseases in China: implications for surveillance and population health policy

This study aimed to analyse trends in notifiable infectious diseases in China, in their historical context. Both English and Chinese literature was searched and diseases were categorised according to the type of disease or transmission route. Temporal trends of morbidity and mortality rates were calculated for eight major infectious diseases types. Strong government commitment to public health responses and improvements in quality of life has led to the eradication or containment of a wide range of infectious diseases in China. The overall infectious diseases burden experienced a dramatic drop during 1975-1995, but since then, it reverted and maintained a gradual upward trend to date. Most notifiable diseases are contained at a low endemic level; however, local small-scale outbreaks remain common. Tuberculosis, as a bacterial infection, has re-emerged since the 1990s and has become prevalent in the country. Sexually transmitted infections are in a rapid, exponential growth phase, spreading from core groups to the general population. Together human immunodeficiency virus (HIV), they account for 39% of all death cases due to infectious diseases in China in 2008. Zoonotic infections, such as severe acute respiratory syndrome (SARS), rabies and influenza, pose constant threats to Chinese residents and remain the most deadly disease type among the infected individuals. Therefore, second-generation surveillance of behavioural risks or vectors associated with pathogen transmission should be scaled up. It is necessary to implement public health interventions that target HIV and relevant coinfections, address transmission associated with highly mobile populations, and reduce the risk of cross-species transmission of zoonotic pathogens.

Molecular epidemiology of measles virus in Iran 2009-2010: first detection of measles genotype H1

Measles virus (MV) genotyping is an important component of measles surveillance in the context of monitoring immunization program effectiveness and documenting MV elimination. The molecular epidemiology and genetic variability of circulating MV strains in Iran during the 2009-2010 were studied in consecutive MV isolates from throat swab and urine. Sequence information obtained from 41 cases based on the 456 nucleotides of the most variable region of the C-terminal part of the N-protein revealed that these sequences belonged to two different genotypes. This is the first description of the genetic characterization of sporadic MV genotype H1 cases in northern Iran. Cases were probably linked to MV importation from distant parts of Asia. The genotype H1 has not been detected in the Eastern Mediterranean Region. In addition, both sequence analysis and epidemiologic data indicated that the more recently detected genotype D4 viruses in Iran were related very closely to viruses that were detected in Pakistan, suggesting that these viruses may have been imported from Pakistan. J. Med. Virol. 83:2200-2207, 2011. © 2011 Wiley Periodicals, Inc.

Phylogenetic analysis of the nucleoprotein gene of measles viruses prevalent in Nantong, Jiangsu Province, China, during 2010

Measles control in China is monitored in part by surveillance of circulating wild-type viruses. The objective of this study was genetic characterization and phylogenetic analysis of measles strains in the Nantong City region of Jiangsu province, China, during 2010. Sera from suspected cases were tested for IgM antibodies and measles virus isolated by inoculation of transport medium onto Vero/SLAM cells. Isolated strains were phylogenetically analysed according to the nucleotide sequence of the C-terminal region of the nucleoprotein gene amplified by RT-PCR. The results revealed 34 cases confirmed by positive IgM, for an incidence of 0·45/100 000. Six isolates identified were all clustered within genotype H1. The findings reported here support continued endemic transmission of measles virus in China.

Emergence and transmission pathways of rapidly evolving evolutionary branch C4a strains of human enterovirus 71 in the Central Plain of China

Background

Large-scale outbreaks of hand, foot, and mouth disease (HFMD) occurred repeatedly in the Central Plain of China (Shandong, Anhui, and Henan provinces) from 2007 until now. These epidemics have increased in size and severity each year and are a major public health concern in mainland China.

Principal Findings

Phylogenetic analysis was performed and a Bayesian Markov chain Monte Carlo tree was constructed based on the complete VP1 sequences of HEV71 isolates. These analyses showed that the HFMD epidemic in the Central Plain of China was caused by at least 5 chains of HEV71 transmission and that the virus continued to circulate and evolve over the winter seasons between outbreaks. Between 1998 and 2010, there were 2 stages of HEV71 circulation in mainland China, with a shift from evolutionary branch C4b to C4a in 2003–2004. The evolution rate of C4a HEV71 was 4.99×10^-3 substitutions per site per year, faster than the mean of all HEV71 genotypes. The most recent common ancestor estimates for the Chinese clusters dated to October 1994 and November 1993 for the C4a and C4b evolutionary branches, respectively. Compared with all C4a HEV71 strains, a nucleotide substitution in all C4b HEV71 genome (A to C reversion at nt2503 in the VP1 coding region, which caused amino acid substitution of VP1–10: Gln to His) had reverted.

Conclusions

The data suggest that C4a HEV71 strains introduced into the Central Plain of China are responsible for the recent outbreaks. The relationships among HEV71 isolates determined from the combined sequence and epidemiological data reveal the underlying seasonal dynamics of HEV71 circulation. At least 5 HEV71 lineages circulated in the Central Plain of China from 2007 to 2009, and the Shandong and Anhui lineages were found to have passed through a genetic bottleneck during the low-transmission winter season.

Molecular epidemiology of measles in India, 2005-2010

Measles is a childhood disease that causes great morbidity and mortality in India and worldwide. Because measles surveillance in India is in its infancy, there is a paucity of countrywide data on circulating Measles virus genotypes. This study was conducted in 21 of 28 States and 2 of 7 Union Territories of India by MeaslesNetIndia, a national network of 27 centers and sentinel practitioners. MeaslesNetIndia investigated 52 measles outbreaks in geographically representative areas from 2005 through June 2010. All outbreaks were serologically confirmed by detection of antimeasles virus immunoglobulin M (IgM) antibodies in serum or oral fluid samples. Molecular studies, using World Health Organization (WHO)-recommended protocols obtained 203 N-gene, 40 H-gene, and 4 M-gene sequences during this period. Measles genotypes D4, D7, and D8 were found to be circulating in various parts of India during the study period. Further phylogenetic analysis revealed 4 lineages of Indian D8 genotypes: D8a, D8b, D8c, and D8d. This study generated a large, countrywide sequence database that can form the baseline for future molecular studies on measles virus transmission pathways in India. This study has created support and capabilities for countrywide measles molecular surveillance that must be carried forward.

Risk analysis for measles reintroduction after global certification of eradication

BACKGROUND

Measles virus will continue to exist after certification of global eradication as virus stocks and infectious materials held in laboratories, in persistently and chronically infected individuals, and possibly in undetected foci of transmission. A literature search was undertaken to identify and evaluate the main risks for reintroduction of measles transmission in the absence of universal measles immunization.

METHODS

A qualitative risk assessment was conducted following a series of literature searches using the PubMed database.

RESULTS

If the criteria for global certification of eradication are stringent and require rigorous validation, then the risk of undetected measles transmission after certification is very low. Risk of unintentional reintroduction from any source, including persistent infections and laboratory materials is low to very low but depends on the extent of measles vaccine use. If immunization levels decrease, measles will become a credible agent for bioterrorism through intentional release.

CONCLUSIONS

Posteradication risks are low and should not deter any attempt at measles eradication. More information on measles transmission dynamics and the role of atypical infections is required to determine requirements for global certification of eradication. Posteradication risks would be minimized through development and implementation of an international risk management strategy, including requirements for a posteradication vaccine stockpile.

Measles virus strain diversity, Nigeria and Democratic Republic of the Congo

Differences in epidemiologic patterns are only partially explained by vaccination practices.

We investigated the genetic diversity of measles virus (MV) in Nigeria (2004–2005) and the Democratic Republic of the Congo (DRC) (2002–2006). Genotype B3 strains circulating in Kinshasa, DRC, in 2002–2003 were fully replaced by genotype B2 in 2004 at the end of the second Congo war. In Nigeria (2004–2005), two genetic clusters of genotype B3, both of which were most closely related to 1 variant from 1998, were identified. Longitudinal analysis of MV strain diversity in Nigeria suggested that only a few of the previously described 1997–1998 variants had continued to circulate, but this finding was concomitant with a rapid restoration of genetic diversity, probably caused by low vaccination coverage and high birth rates. In contrast, the relatively low genetic diversity of MV in DRC and the genotype replacement in Kinshasa reflect a notable improvement in local measles control.

Comparison of laboratory diagnostic methods for measles infection and identification of measles virus genotypes in Hong Kong

The sensitivities of IgM detection, virus isolation, and RT-PCR for the diagnosis of measles infection were assessed using samples collected from confirmed measles cases from 2006 to 2009. The optimal timing of specimen collection and the preferred specimen type(s) for these tests were also determined. IgM detection showed highest sensitivity when serum samples were collected >or=5 days after rash onset. Virus isolation gave the highest sensitivity when samples were collected <or=3 days after rash onset, with nasopharyngeal aspirate being the best specimen type, followed by urine and throat/combined throat and nasal swab. The highest RT-PCR positive rate (81.0%) was obtained with serum samples collected <or=3 days after rash onset. RT-PCR positive rate of 100% was observed with throat/combined throat and nasal swab, urine and nasopharyngeal aspirate collected <or=16, 4-16, and 4-7 days after rash onset, respectively. The genotype of each measles case was confirmed by sequencing. It was shown that the predominant measles viruses detected in Hong Kong during 2006-2009 belonged to genotype H1 (subtype a) and these strains were related closely to those detected in China.

Absence of endemic measles transmission in a highly vaccinated population from 1999 to 2008: implications of sustained measles elimination in Taiwan

BACKGROUND

Measles remains a leading vaccine-preventable cause of child mortality worldwide. The impact of vaccination programs can be seen in the increasingly low incidence of measles. However, cases of measles continue to occur in low numbers every year in Taiwan. We assessed the epidemiology of measles in Taiwan from 1999 to 2008 with a focus on domestic versus imported cases.

METHODS

We analyzed the data reported to surveillance systems at the Taiwan Center for Disease Control, where viral isolation was performed.

RESULTS

A total of 84 measles cases were reported from 1999 to 2008 in Taiwan with the incidence of measles varying from 0 to 1.5 per 1,000,000 people per year, peaking in 2002 and again in 2008. The incidence decreased with increasing age in both males and females. Among the 84 reported measles cases, 39 (46%) originated internationally, 8 (10%) were epidemiologically linked to imported cases and the source was unknown in 37 (44%) of the cases. The unknown-source cases were analyzed for potential evidence of endemic measles transmission. Most of the measles cases that occurred in Taiwan from 1999 to 2008 were associated with imported cases. No endemic transmission of measles in Taiwan was identified.

CONCLUSIONS

This study suggests that maintaining the high rate of vaccination coverage is needed to prevent future outbreak and sustain the elimination of measles in Taiwan.

New measles virus genotype associated with outbreak, China

To determine the origin of the virus associated with a measles outbreak in Menglian County, Yunnan Province, People's Republic of China, in 2009, we conducted genetic analyses. Phylogenetic analyses based on nucleoprotein (N) and hemagglutinin (H) gene sequences showed that these Menglian viruses were not closely related to sequences of any World Health Organization (WHO) reference strains representing the 23 currently recognized genotypes. The minimum nucleotide divergence between the Menglian viruses and the most closely related reference strain, genotype D7, was 3.3% for the N gene and 3.0% for the H gene. A search of the databases of GenBank, WHO, and the Health Protection Agency Measles Nucleotide Surveillance showed that the Menglian viruses, together with the 2 older non-Menglian viruses, could be members of a new proposed measles genotype, d11. The new genotype designation will allow for better description of measles transmission patterns, especially in the Southeast Asian and Western Pacific regions.

Genetic characterization of wild-type measles viruses isolated in China, 2006-2007

Molecular characterization of wild-type measles viruses in China during 1995-2004 demonstrated that genotype H1 was endemic and widely distributed throughout the country. H1-associated cases and outbreaks caused a resurgence of measles beginning in 2005. A total of 210,094 measles cases and 101 deaths were reported by National Notifiable Diseases Reporting System (NNDRS) and Chinese Measles Laboratory Network (LabNet) from 2006 to 2007, and the incidences of measles were 6.8/100,000 population and 7.2/100,000 population in 2006 and 2007, respectively. Five hundred and sixty-five wild-type measles viruses were isolated from 24 of 31 provinces in mainland China during 2006 and 2007, and all of the wild type virus isolates belonged to cluster 1 of genotype H1. These results indicated that H1-cluster 1 viruses were the predominant viruses circulating in China from 2006 to 2007. This study contributes to previous efforts to generate critical baseline data about circulating wild-type measles viruses in China that will allow molecular epidemiologic studies to help measure the progress made toward China's goal of measles elimination by 2012.

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.

Protocols for sampling viral sequences to study epidemic dynamics

With more emphasis being put on global infectious disease monitoring, viral genetic data are being collected at an astounding rate, both within and without the context of a long-term disease surveillance plan. Concurrent with this increase have come improvements to the sophisticated and generalized statistical techniques used for extracting population-level information from genetic sequence data. However, little research has been done on how the collection of these viral sequence data can or does affect the efficacy of the phylogenetic algorithms used to analyse and interpret them. In this study, we use epidemic simulations to consider how the collection of viral sequence data clarifies or distorts the picture, provided by the phylogenetic algorithms, of the underlying population dynamics of the simulated viral infection over many epidemic cycles. We find that sampling protocols purposefully designed to capture sequences at specific points in the epidemic cycle, such as is done for seasonal influenza surveillance, lead to a significantly better view of the underlying population dynamics than do less-focused collection protocols. Our results suggest that the temporal distribution of samples can have a significant effect on what can be inferred from genetic data, and thus highlight the importance of considering this distribution when designing or evaluating protocols and analysing the data collected thereunder.

Molecular evolution of measles viruses circulated in Taiwan 1992-2008

Genetic analyses of viral samples from 74 laboratory confirmed measles cases occurring in Taiwan during 1992-2008 identified six viral genotypes D3, D5, D9, G2, H1 and H2. The most frequently detected genotype, H1, was associated with outbreaks in 1994 and 2002, and was the likely indigenous genotype in 1992. In response to the outbreaks, two catch-up campaigns were launched and a routine second dose of measles, mumps, and rubella vaccine at entry to elementary school was introduced. The vaccination campaigns successfully reduced the number of measles cases in Taiwan, and many of the more recent cases can be traced to importations, primarily from other Asian countries. A number of measles genotypes which were associated with outbreaks in other Asian countries were detected among the more recent cases. The more recent genotype H1 viruses had sequences that were identical to those currently circulating in China or associated with international importation of virus.

Measles resurgence associated with continued circulation of genotype H1 viruses in China, 2005

Measles morbidity and mortality decreased significantly after measles vaccine was introduced into China in 1965. From 1995 to 2004, average annual measles incidence decreased to 5.6 cases per 100,000 population following the establishment of a national two-dose regimen. Molecular characterization of wild-type measles viruses demonstrated that genotype H1 was endemic and widely distributed throughout the country in China during 1995-2004. A total of 124,865 cases and 55 deaths were reported from the National Notifiable Diseases Reporting System (NNDRS) in 2005, which represented a 69.05% increase compared with 2004. Over 16,000 serum samples obtained from 914 measles outbreaks and the measles IgM positive rate was 81%. 213 wild-type measles viruses were isolated from 18 of 31 provinces in China during 2005, and all of the isolates belonged to genotype H1. The ranges of the nucleotide sequence and predicted amino acid sequence homologies of the 213 genotype H1 strains were 93.4%-100% and 90.0%-100%, respectively. H1-associated cases and outbreaks caused the measles resurgence in China in 2005. H1 genotype has the most inner variation within genotype, it could be divided into 2 clusters, and cluster 1 viruses were predominant in China throughout 2005.

Genetic characterization of Chinese measles vaccines by analysis of complete genomic sequences

The complete genomic sequences of two Chinese measles vaccine viruses, Shanghai-191 (S-191) and Changchun-47 (C-47), were determined and compared to the sequences of other measles vaccine strains as well as the prototype measles strain, Edmonston wild-type (Edwt). Compared to Edwt, S-191 and C-47 had 49 and 43 nucleotide changes, respectively. These differences were found at 52 nucleotide positions that were not found in other vaccine strains. Phylogenetic analysis of the all of the available genomic sequences for measles vaccines showed that S-191 and C-47 were most closely related to the Leningrad-4 strain. S-191 and C-47 shared conserved vaccine virus-specific amino acid changes in the phosphoprotein (P), V, C, matrix (M), and hemagglutinin (H) that could represent important targets for future studies aimed at understanding the molecular basis of attenuation. In addition, S-191 and C-47 had several unique amino acid changes including 13 positions that differed from Edwt. This is the first comparison of the complete genomic sequences of Chinese measles vaccines to the sequences of other vaccine strains.

Genetic characterization of measles viruses in China, 2004

Genetic characterization of wild-type measles virus was studied using nucleotide sequencing of the C-terminal region of the N protein gene and phylogenetic analysis on 59 isolates from 16 provinces of China in 2004. The results showed that all of the isolates belonged to genotype H1. 51 isolates were belonged to cluster 1 and 8 isolates were cluster 2 and Viruses from both clusters were distributed throughout China without distinct geographic pattern. The nucleotide sequence and predicted amino acid homologies of the 59 H1 strains were 96.5%-100% and 95.7%-100%, respectively. The report showed that the transmission pattern of genotype H1 viruses in China in 2004 was consistent with ongoing endemic transmission of multiple lineages of a single, endemic genotype. Multiple transmission pathways leaded to multiple lineages within endemic genotype.

Clinical and genetic characterization of measles viruses isolated from adult patients in Shanghai in 2006

BACKGROUND

In recent years there has been an increase in adult measles cases in Shanghai, and an outbreak occurred in 2005. Although there have been many studies analyzing the genotype of measles virus from pediatric patients in various parts of China, there is little information on the clinical findings and genetic makeup of adult measles.

OBJECTIVES

Clinical information and phylogenetic analysis of adult measles infection in Shanghai.

STUDY DESIGN

Blood, urine, throat swabs, and clinical information were collected from adult measles patients reporting to three major hospitals in Shanghai. Measles virus was isolated in Vero-SLAM cells. The C-terminus of the N gene of the isolates was sequenced and analyzed with reference to sequences obtained from GenBank.

RESULTS

More than half of the patients developed severe clinical symptoms. None of the patients knew their measles vaccination history. All measles virus isolates had the same amino acid substitutions as the two standard H1a measles strains at position 484 and were classified as H1a genotype and could be further divided into three small clusters.

CONCLUSIONS

The genotype of the predominant measles virus causing disease in adults in Shanghai is H1a.