TY - JOUR T1 - Co-circulating mumps lineages at multiple geographic scales JF - bioRxiv DO - 10.1101/343897 SP - 343897 AU - Shirlee Wohl AU - Hayden C. Metsky AU - Stephen F. Schaffner AU - Anne Piantadosi AU - Meagan Burns AU - Joseph A. Lewnard AU - Bridget Chak AU - Lydia A. Krasilnikova AU - Katherine J. Siddle AU - Christian B. Matranga AU - Bettina Bankamp AU - Scott Hennigan AU - Brandon Sabina AU - Elizabeth H. Byrne AU - Rebecca J. McNall AU - Daniel J. Park AU - Soheyla Gharib AU - Susan Fitzgerald AU - Paul Barriera AU - Stephen Fleming AU - Susan Lett AU - Paul A. Rota AU - Lawrence C. Madoff AU - Bronwyn L. MacInnis AU - Nathan L. Yozwiak AU - Sandra Smole AU - Yonatan H. Grad AU - Pardis C. Sabeti Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/06/12/343897.abstract N2 - Despite widespread vaccination, eleven thousand mumps cases were reported in the United States (US) in 2016–17, including hundreds in Massachusetts, primarily in college settings. We generated 203 whole genome mumps virus (MuV) sequences from Massachusetts and 15 other states to understand the dynamics of mumps spread locally and nationally, as well as to search for variants potentially related to vaccination. We observed multiple MuV lineages circulating within Massachusetts during 2016–17, evidence for multiple introductions of the virus to the state, and extensive geographic movement of MuV within the US on short time scales. We found no evidence that variants arising during this outbreak contributed to vaccine escape. Combining epidemiological and genomic data, we observed multiple co-circulating clades within individual universities as well as spillover into the local community. Detailed data from one well-sampled university allowed us to estimate an effective reproductive number within that university significantly greater than one. We also used publicly available small hydrophobic (SH) gene sequences to estimate migration between world regions and to place this outbreak in a global context, but demonstrate that these short sequences, historically used for MuV genotyping, are inadequate for tracing detailed transmission. Our findings suggest continuous, often undetected, circulation of mumps both locally and nationally, and highlight the value of combining genomic and epidemiological data to track viral disease transmission at high resolution. ER -