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PLoS Biol. 2020 Feb 11;18(2):e3000611. doi: 10.1371/journal.pbio.3000611. eCollection 2020 Feb.

Combining genomics and epidemiology to track mumps virus transmission in the United States.

Author information

1
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
2
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
3
Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
4
Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America.
5
Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America.
6
Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America.
7
Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America.
8
Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
9
Harvard University Health Services, Harvard University, Cambridge, Massachusetts, United States of America.
10
Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.
11
Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America.
12
Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.
13
Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America.

Abstract

Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks. We paired epidemiological data from public health investigations with analysis of mumps virus whole genome sequences from 201 infected individuals, focusing on Massachusetts university communities. Our analysis suggests continuous, undetected circulation of mumps locally and nationally, including multiple independent introductions into Massachusetts and into individual communities. Despite the presence of these multiple mumps virus lineages, the genomic data show that one lineage has dominated in the US since at least 2006. Widespread transmission was surprising given high vaccination rates, but we found no genetic evidence that variants arising during this outbreak contributed to vaccine escape. Viral genomic data allowed us to reconstruct mumps transmission links not evident from epidemiological data or standard single-gene surveillance efforts and also revealed connections between apparently unrelated mumps outbreaks.

Conflict of interest statement

The authors have declared that no competing interests exist.

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