{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T05:56:09Z","timestamp":1791870969062,"version":"4.3.4"},"reference-count":32,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T00:00:00Z","timestamp":1778544000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004423","name":"WHO","doi-asserted-by":"publisher","award":["2025\/1577838"],"award-info":[{"award-number":["2025\/1577838"]}],"id":[{"id":"10.13039\/100004423","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Madagascar experienced a severe measles epidemic between September 2018 and mid-2019, resulting in more than 146,000 cases and 1200 deaths, primarily among children under 15 years of age. This epidemic occurred in a context of low vaccination coverage. Prior to this outbreak, no genotyping data were available for the measles virus (MeV) or rubella virus (RuV) in Madagascar. This study aimed to molecularly characterize MeV and RuV strains circulating during the epidemic. A total of 310 biological samples (gingival swabs, urine, and stool) were collected from 288 suspected cases with a mean age of 11.4 years. Viral detection was performed using real-time RT-PCR, followed by conventional RT-PCR and sequencing of the N and H genes for MeV and of the E1 gene for RuV. Co-circulation of the two viruses was observed, with positivity rates of 39.9% (115\/288) for MeV and 40.0% (70\/175) for RuV. The mean age differed significantly between MeV-positive (12.0 years) and RuV-positive (7.2 years) patients, with 35.1% and 43.8% of cases occurring in children under five years of age, respectively. Phylogenetic analysis showed that all MeV strains belonged to genotype [B3], and they were highly similar to strains circulating globally in 2018\u20132019, suggesting recent introduction. In contrast, all RuV strains belonged to genotype [2B] and displayed greater genetic diversity, consistent with endemic rubella circulation in a partially vaccinated or unvaccinated population. This study provides the first genotyping data for Madagascar essential for monitoring virus circulation and supporting elimination efforts in the African region.<\/jats:p>","DOI":"10.3390\/pathogens15050514","type":"journal-article","created":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T13:11:31Z","timestamp":1779196291000},"page":"514","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Molecular Characterization of Measles and Rubella Virus Strains from the 2018\u20132019 Epidemic in Madagascar"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7688-4832","authenticated-orcid":false,"given":"Richter","family":"Razafindratsimandresy","sequence":"first","affiliation":[{"name":"Unit\u00e9 de Virologie, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0415-3234","authenticated-orcid":false,"given":"Jonhson","family":"Raharinantoanina","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel","family":"Andrianiriana","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja Elsam","family":"Andrianjakatsilavo","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-9920-7387","authenticated-orcid":false,"given":"Arv\u00e9","family":"Ratsimbazafy","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-7069-7228","authenticated-orcid":false,"given":"Laurence","family":"Randrianasolo","sequence":"additional","affiliation":[{"name":"Unit\u00e9 d\u2019Epid\u00e9miologie et de Recherche Clinique, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2063-3932","authenticated-orcid":false,"given":"Norosoa Harline","family":"Razanajatovo","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6397-836X","authenticated-orcid":false,"given":"Soa Fy","family":"Andriamandimby","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1107-0859","authenticated-orcid":false,"given":"Jean Michel","family":"Heraud","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3173-4053","authenticated-orcid":false,"given":"Vincent","family":"Lacoste","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar"},{"name":"D\u00e9partement de Virologie, Institut Pasteur, 75724 Paris Cedex 15, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"S514","DOI":"10.1093\/infdis\/jir118","article-title":"Global distribution of measles genotypes and measles molecular epidemiology","volume":"204","author":"Rota","year":"2011","journal-title":"J. Infect. Dis."},{"key":"ref_2","unstructured":"WHO (2012). Measles virus nomenclature update: 2012. Relev. Epidemiol. Hebd., 87, 73\u201381."},{"key":"ref_3","unstructured":"CDC (2025, May 23). Rubella (German Measles, Three-Day Measles), Available online: https:\/\/www.cdc.gov\/rubella\/index.html."},{"key":"ref_4","unstructured":"World Health Organization (2012). Global Measles and Rubella Strategic Plan: 2012\u20132020, WHO."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2417","DOI":"10.1007\/s00705-019-04306-w","article-title":"Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)","volume":"164","author":"Walker","year":"2019","journal-title":"Arch. Virol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e02349-20","DOI":"10.1128\/JVI.02349-20","article-title":"Molecular and Structural Insights into the Life Cycle of Rubella Virus","volume":"95","author":"Das","year":"2021","journal-title":"J. Virol."},{"key":"ref_7","unstructured":"WHO (2013). Rubella virus nomenclature update: 2013. Relev. Epidemiol. Hebd., 88, 337\u2013343."},{"key":"ref_8","unstructured":"WHO (1998). Expanded Programme on Immunization (EPI). Standardization of the nomenclature for describing the genetic characteristics of wild-type measles viruses. Relev. Epidemiol. Hebd., 73, 265\u2013269."},{"key":"ref_9","unstructured":"World Health Organization (2001). Measles: Mortality Reduction and Regional Elimination: Strategic Plan 2001\u20132005, WHO."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"20","DOI":"10.11604\/pamj.2020.37.20.24530","article-title":"Madagascar 2018\u20132019 measles outbreak response: Main strategic areas","volume":"37","author":"Sodjinou","year":"2020","journal-title":"Pan Afr. Med. J."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.jviromet.2005.10.006","article-title":"Development of quantitative gene-specific real-time RT-PCR assays for the detection of measles virus in clinical specimens","volume":"132","author":"Hummel","year":"2006","journal-title":"J. Virol. Methods"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"114500","DOI":"10.1016\/j.jviromet.2022.114500","article-title":"Development of a rapid, internally controlled, two target, real-time RT-PCR for detection of rubella virus","volume":"303","author":"Schulz","year":"2022","journal-title":"J. Virol. Methods"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"311","DOI":"10.3201\/eid1002.030759","article-title":"Real-time reverse transcription-polymerase chain reaction assay for SARS-associated coronavirus","volume":"10","author":"Emery","year":"2004","journal-title":"Emerg. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Kim, J.M., Park, S., Kim, S., Park, K.R., Wang, J.S., and Chung, Y.S. (2021). Genetic Analysis of the Measles Virus From the Outbreaks in South Korea, 2019. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.763107"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2107","DOI":"10.1002\/jmv.23935","article-title":"Phylogenetic analysis of rubella viruses identified in Uganda, 2003\u20132012","volume":"86","author":"Namuwulya","year":"2014","journal-title":"J. Med. Virol."},{"key":"ref_16","unstructured":"WHO (2005). Standardization of the nomenclature for genetic characteristics of wild-type rubella viruses. Relev. Epidemiol. Hebd., 80, 126\u2013132."},{"key":"ref_17","unstructured":"WHO (2006). Global distribution of measles and rubella genotypes\u2014update. Relev. Epidemiol. Hebd., 81, 474\u2013479."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Xu, S., Zhang, Y., Zhu, Z., Liu, C., Mao, N., Ji, Y., Wang, H., Jiang, X., Li, C., and Tang, W. (2013). Genetic characterization of the hemagglutinin genes of wild-type measles virus circulating in china, 1993\u20132009. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0073374"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e003153","DOI":"10.1136\/bmjgh-2020-003153","article-title":"Towards better targeting: Lessons from a posthoneymoon measles outbreak in Madagascar, 2018\u20132019","volume":"5","author":"Raherindrasana","year":"2020","journal-title":"BMJ Glob. Health"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2219","DOI":"10.1093\/aje\/kwy114","article-title":"Revealing Measles Outbreak Risk With a Nested Immunoglobulin G Serosurvey in Madagascar","volume":"187","author":"Winter","year":"2018","journal-title":"Am. J. Epidemiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1128\/CVI.00084-13","article-title":"Nonfebrile seizures after mumps, measles, rubella, and varicella-zoster virus combination vaccination with detection of measles virus RNA in serum, throat, and urine","volume":"20","author":"Eckerle","year":"2013","journal-title":"Clin. Vaccine Immunol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1002\/jmv.25407","article-title":"Laboratory-based investigation of fever with rash cases in the Maharashtra State-India, 2014 to 2017","volume":"91","author":"Vaidya","year":"2019","journal-title":"J. Med. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1867","DOI":"10.1002\/jmv.24548","article-title":"Towards measles elimination: Phylogenetic analysis of measles viruses in Turkey (2012\u20132013) and identification of genotype D8","volume":"88","author":"Kalaycioglu","year":"2016","journal-title":"J. Med. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1002\/jmv.22244","article-title":"Molecular characterization of wild-type measles viruses in Tamil Nadu, India, during 2005\u20132006: Relationship of genotype D8 strains from Tamil Nadu to global strains","volume":"84","author":"Duraisamy","year":"2012","journal-title":"J. Med. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1186\/1743-422X-9-237","article-title":"Identification of different lineages of measles virus strains circulating in Uttar Pradesh, North India","volume":"9","author":"Shakya","year":"2012","journal-title":"Virol. J."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1002\/jmv.24702","article-title":"Measles virus genotypes circulating in India, 2011\u20132015","volume":"89","author":"Vaidya","year":"2017","journal-title":"J. Med. Virol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1186\/1743-422X-9-284","article-title":"Molecular epidemiology of measles virus in Italy, 2002\u20132007","volume":"9","author":"Magurano","year":"2012","journal-title":"Virol. J."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"acmi000093","DOI":"10.1099\/acmi.0.000093","article-title":"Laboratory methods supporting measles surveillance in Queensland, Australia, 2010\u20132017","volume":"2","author":"McMahon","year":"2020","journal-title":"Access Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Oude Munnink, B.B., Phan, M.V., Kellam, P., Cotten, M., and Consortium, V. (2016). Complete Genome Characterization of Two Wild-Type Measles Viruses from Vietnamese Infants during the 2014 Outbreak. Genome Announc., 4.","DOI":"10.1128\/genomeA.00250-16"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1002\/jmv.20959","article-title":"Molecular characterization of measles virus circulating in the Indian Ocean Islands during 2005\u20132006 and in France in 2006","volume":"79","author":"Landreau","year":"2007","journal-title":"J. Med. Virol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"104257","DOI":"10.1016\/j.jcv.2019.104257","article-title":"Comparison of virological and serological methods for laboratory confirmation of rubella","volume":"123","author":"Uchino","year":"2020","journal-title":"J. Clin. Virol."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/5\/514\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T13:30:23Z","timestamp":1779197423000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/5\/514"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,12]]},"references-count":32,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["pathogens15050514"],"URL":"https:\/\/doi.org\/10.3390\/pathogens15050514","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,12]]}}}