Molecular epidemiology and changing distribution of genotypes of measles virus field strains in Japan.
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ABSTRACT:
SUBMITTER: Katayama Y
PROVIDER: S-EPMC230028 | biostudies-other | 1997 Oct
REPOSITORIES: biostudies-other
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Project description: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.
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Project description:BackgroundThe European Regional Office of the World Health Organization (WHO/Europe) developed a strategic approach to halt the indigenous transmission of measles in its 53 Member States by 2015. In view of the goal of measles elimination, it is of great importance to assess the circulation of wild-type measles virus (MV). Genetic analysis is indispensable to understand the epidemiology of measles.MethodsUrine and saliva samples were collected between May 2002 and December 2007, in order to find the origins and routes of wild type measles virus circulation. RT-PCR was performed on a total of 414 clinical samples of patients from different Italian regions. The results confirmed the genome presence in 199 samples, out of which 179 were sequenced. The sequences were genotyped by comparing the fragment coding for the carboxyl terminus of the nucleoprotein (450 nucleotides) with that one of the WHO reference strains.ResultsFrom the year 2002 to the year 2007 phylogenetic analysis of measles sequences showed a predominant circulation of the D7 genotype in the Italian territory for the years 2002-2004. This genotype was replaced by D4 and B3 genotypes in the biennium 2006-2007. During the same period C2, A, D5 and D8 genotypes were also detected.ConclusionsGenetic characterization of wild-type MV provides a means to study the transmission pathways of the virus, and is an essential component of laboratory-based surveillance. Knowledge of currently circulating measles virus genotype in Italy will help in monitoring the success of the measles elimination programme and will contribute to evaluate the effectiveness of future vaccination campaigns.
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Project description: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.
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Project description:A nationwide rubella epidemic occurred from 2012 to 2013 in Japan, resulting in around 17,000 rubella cases and the birth of 45 infants with congenital rubella syndrome. The aim of this study was to genetically characterize the rubella viruses (RVs) circulating around the time of the epidemic in Japan. In total, 221 RV strains detected from 14 prefectures in Japan between 2010 and 2014 were sequenced in the 739 nucleotide-window region within the E1 gene. The virus strains were chronologically and geographically characterized into groups based on phylogenetic analysis. Among the 221 strains analyzed, 192 (87%), 26 (12%), and 3 (1%) strains were classified into genotypes 2B, 1E, and 1J, respectively. The majority (n = 184) of the genotype 2B strains belonged to lineage 2B-L1 and shared nucleotide homology with the strains detected in Southeast and East Asian countries. Phylogenetic analyses demonstrated that at least six distinct clusters of RV strains (clusters 1-6) induced outbreaks in Japan between 2010 and 2014. Among them, strains from clusters 3, 4, and 6 circulated almost simultaneously during 2012-2013. The cluster 3 strains circulated locally, whereas strains from cluster 4 spread nationwide. The findings suggest that RVs were introduced into Japan many times from neighboring countries. The 2012-2013 epidemic was a complex of outbreaks induced by at least three clusters of RV strains.
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Project description:To evaluate the changes in respiratory syncytial virus (RSV) collected between 2019 and 2022, we analyzed RSV-A and RSV-B strains from various prefectures in Japan before and after the COVID-19 pandemic. RT-PCR-positive samples collected from children with rapid test positivity at outpatient clinics in 11 prefectures in Japan were sequenced for the ectodomain of the G gene to determine the genotype. Time-aware phylogeographic analyses were performed using the second hypervariable region (HVR) of the G gene from 2012 to 2022. Of 967 samples, 739 (76.4%) were found to be RSV-positive using RT-PCR. RSV peaked in September 2019 but was not detected in 2020, except in Okinawa. Nationwide epidemics occurred with peaks in July 2021 and 2022. The genotype remained the same, ON1 for RSV-A and BA9 for RSV-B during 2019-2022. Phylogeographic analysis of HVR revealed that at least seven clusters of RSV-A had circulated previously but decreased to two clusters after the pandemic, whereas RSV-B had a single monophyletic cluster over the 10 years. Both RSV-A and RSV-B were transferred from Okinawa into other prefectures after the pandemic. The RSV epidemic was suppressed due to pandemic restrictions; however, pre-pandemic genotypes spread nationwide after the pandemic.
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Project description:BackgroundMolecular epidemiology of measles virus (MV) is important, not only to measure the success of measles vaccination programs but also to monitor the circulation and elimination of the virus worldwide. In this study, we compared MV obtained from patients before the 2003 mass vaccination MR campaign and viruses detected after 2003 until 2008 in Iran.MethodsThe nucleoprotein (N) gene of 29 MV strains circulating in Iran between 2002 and 2008 were amplified by RT-PCR and subjected to sequence and phylogenetic analysis.ResultsMolecular characterization of MV studied here revealed that although the outbreaks in Iran were associated with MV genotype D4, the isolated viruses clearly belonged to several different lineages. Maximum and minimum homology within the 29 Iranian strains in our study was100% and 94.9% within the carboxyl terminus of the N gene, respectively. Using ClustalX program, the alignment of Iranian MV sequences showed nine lineages.ConclusionThis study provides the usefulness of MV sequence analysis for the demonstration of local interruption of indigenous strain transmission as well as providing a valuable means for monitoring the elimination processes of MV control.
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Project description:Molecular epidemiological investigation of measles outbreaks can document the interruption of endemic measles transmission and is useful for establishing and clarifying epidemiological links between cases in geographically distinct clusters. To determine the distribution of measles virus genotypes in the prevaccine and postvaccine eras, a literature search of biomedical databases, measles surveillance websites and other electronic sources was conducted for English language reports of measles outbreaks or genetic characterization of measles virus isolates. Genotype assignments based on classification systems other than the currently accepted WHO nomenclature were reassigned using the current criteria. This review gives a comprehensive overview of the distribution of MV genotypes in the prevaccine and postvaccine eras and describes the geographically diverse distribution of some measles virus genotypes and the localized distributions of other genotypes.
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