12While measles remains endemic in parts of the world, efforts to eliminate measles 13 transmission continue, and viral sequence data may shed light on progress towards these 14 goals. Genetic diversity has been used as a proxy for disease prevalence; however, 15 seasonally-driven disease dynamics are typically characterized by deep population 16 bottlenecks between epidemics, which severely disrupt the genetic signal. Here, we simulate 17 measles metapopulation dynamics, and show that it is the population bottleneck, rather than 18 epidemic size, which plays the largest role in observed pathogen diversity. While high levels 19 of vaccination greatly reduces measles diversity, paradoxically, diversity increases with 20 intermediate levels of vaccination, despite reducing incidence. We examined diversity and 21 incidence using published data to compare our simulated outcomes with real observations, 22 finding a significant relationship between harmonic mean incidence and genetic diversity. 23 Our study demonstrates that caution should be taken when interpreting pathogen diversity, 24 particularly for short-term, local dynamics. 25 26 scenarios, encompassing biennial and annual outbreaks, as well as chaotic dynamics (9), 53 providing a range of settings to explore how genetic diversity is impacted by population 54 fluctuations. 55 56 Measles virus has just a single serotype, although 24 genotypes have been defined (10) on 57 the basis of (at minimum) the 450-nucleotides coding for the COOH terminal 150 amino 58 acids of the nucleoprotein (N-450) (11). The World Health Organization (WHO) Global 59 Measles and Rubella Laboratory Network supports measles genotyping on a global scale. At 60 present, laboratory confirmation of measles infection is based on detection of virus specific 61 IgM antibodies in serum samples. Though WHO encourages the collection of specimens for 62 virus detection, the quality and completeness of virologic surveillance varies considerably by 63 country and WHO region (12). Classification of strains sampled during an outbreak into 64 these genotypes can provide additional insights into epidemiological dynamics. In many 65 countries with high vaccine coverage, a relatively high turnover of predominant genotypes is 66 observed, since outbreaks are generated by sporadic introductions, and are subsequently 67 either eliminated, or reduced to a low level, allowing new importations of different genotypes 68 to take over (13). In contrast, countries with lower vaccination coverage and endemic 69 measles are more likely to be characterized by a single genotype (14). For instance, 70 measles in China is predominantly caused by genotype H1, with only few importation-71 associated cases identified belonging to other genotypes (15, 16), while genotype D8 72 dominates in India (17). Changes in genotype distribution can be indicative of breaks in 73 transmission and importation (13), and new outbreaks in a previously disease-free 74 population are likely to comprise a single major genotype and...