Session 3: Molecular Epidemiology Introduction Paul Rota Centers for Disease Control Accelerating Progress towards Measles and Rubella Elimination Hotel Royal, Geneva, Switzerland, 21-23 June 2016 *The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention. National Center for Immunization & Respiratory Diseases Division of Viral Diseases

All vaccines strains are in genotype A Lessons Learned from > 20 years of Genetic Characterization of Measles Viruses: 1 All vaccines strains are in genotype A Wild-type viruses in genotype A no longer circulate Sequence information allowed development of RT-PCR based assays for rapid confirmation of vaccines reactions National Center for Immunization & Respiratory Diseases Division of Viral Diseases

Unlikely that antigenic drift will compromise vaccine efficacy Lessons Learned from > 20 years of Genetic Characterization of Measles Viruses: 2 No evidence for selective pressure on the H protein based on measurement of rates on nonsynonymous/synonymous amino acid substitutions Site directed mutagenesis of the measles H protein shows structural constraints needed for binding to SLAM and nectin-4 Unlikely that antigenic drift will compromise vaccine efficacy National Center for Immunization & Respiratory Diseases Division of Viral Diseases

Change in apparent geographic restriction of some genotypes Lessons Learned from > 20 years of Genetic Characterization of Measles Viruses: 3 Genetic characterization allows tracking of viral transmission pathways Extended sequencing windows will be needed to increase the resolution of molecular epidemiologic studies Change in apparent geographic restriction of some genotypes Genotype B3, once restricted to African countries, now has a global distribution Genotype D8, endemic in India, now has a global distribution Genotype H1, still endemic only in China National Center for Immunization & Respiratory Diseases Division of Viral Diseases

Lessons Learned from > 20 years of Genetic Characterization of Measles Viruses: 4 In countries that have eliminated measles, the pattern of genotypes reflects the sources of imported virus Lack of endemic genotype is an essential criterion for verification of elimination Countries with endemic measles have multiple, co circulating lineages of measles virus In countries where measles has been reintroduced, often only a single lineage is detected National Center for Immunization & Respiratory Diseases Division of Viral Diseases

11 Wild-type Genotypes Detected Since 2005: 6 Still Circulating 2006 2007 2008 2009 2010 2011 2012 2013 2014 B2   B3 D11 D4 D5 D6 D7 D8 D9 G3 H1 National Center for Immunization & Respiratory Diseases Division of Viral Diseases

Shift in genotypes over time in various regions Lessons Learned from > 20 years of Genetic Characterization of Measles Viruses: 5 There is an apparent decrease in genetic diversity of circulating measles viruses based on a decrease in the number of genotypes detected Shift in genotypes over time in various regions National Center for Immunization & Respiratory Diseases Division of Viral Diseases

What Does the Decreasing Genetic Diversity of Measles Viruses Tell Us? As the incidence of measles decreases the number of co-circulating lineages decreases. Can this decrease be used to measure the effectiveness of vaccination programs? The shift of genotypes and decrease in number of circulating genotypes suggests that measles transmission is interrupted frequently. However, as the number of measles susceptible individuals in increases, the country/region is reseeded by imported viruses. Though interruption of transmission has been suggested by epidemiologic data in the past, the more recent application of molecular epidemiology has helped to document these interruptions. Examples: Europe (C2, D6, D4, now D8 and B3) The Philippines, 2000-2015, interruption of genotype D3 National Center for Immunization & Respiratory Diseases Division of Viral Diseases

Measles Genotypes In the Philippines 2014-2015 Genotype B3 introduced, genotype B3 and D9 continues to circulate and cause outbreaks 2000-2004 Genotype D3 is the endemic genotype in the Philippines and D3 imports to other countries are traced to the Philippines 2007-2009 Genotypes D9 and G3 introduced and detected in outbreaks Number of measles cases 2004-2005 Measles campaign in 2004, no measles detected in 2005 Genotype D3 not detected globally after 2004 National Center for Immunization & Respiratory Diseases Division of Viral Diseases

Short Summary Genetic characterization of measles virus by the GMRLN has made substantial contributions to both the biology and evolution of measles viruses, and has become and integral prat of routine laboratory surveillance for measles The GMRLN needs to continue to build capacity for genetic characterization of both measles and rubella and to integrate new testing schemes and new technologies