Dynamics of Eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States

Eastern equine encephalitis virus (EEEV) causes a rare but severe disease in horses and humans, and is maintained in an enzootic transmission cycle between songbirds and Culiseta melanura mosquitoes. In 2019, the largest EEEV outbreak in the United States for more than 50 years occurred, centered in the Northeast. To explore the dynamics of the outbreak, we sequenced 80 isolates of EEEV and combined them with existing genomic data. We found that, like previous years, cases were driven by frequent short-lived virus introductions into the Northeast from Florida. Once in the Northeast, we found that Massachusetts was important for regional spread. We found no evidence of any changes in viral, human, or bird factors which would explain the increase in cases in 2019. By using detailed mosquito surveillance data collected by Massachusetts and Connecticut, however, we found that the abundance of Cs. melanura was exceptionally high in 2019, as was the EEEV infection rate. We employed these mosquito data to build a negative binomial regression model and applied it to estimate early season risks of human or horse cases. We found that the month of first detection of EEEV in mosquito surveillance data and vector index (abundance multiplied by infection rate) were predictive of cases later in the season. We therefore highlight the importance of mosquito surveillance programs as an integral part of public health and disease control. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Research reported in this publication was supported by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health under Award Number DP2AI176740 (NDG), CTSA Grant Number UL1 TR001863 from the National Center for Advancing Translational Science (NCATS), a component of the National Institutes of Health (CBFV), the Cooperative Agreement Number U01CK000509 funded by the Centers for Disease Control and Northeast Center of Excellence (PMA, ATC), the KU Leuven Internal Funds Grant No. C14/18/094 (GB), and the Research Foundation - Flanders award “Fonds voor Wetenschappelijk Onderzoek - Vlaanderen,” G0E1420N, G098321N (GB). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Yale University Human Research Protection Program Institutional Review Board waived ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Human and horse case data are available on request to ArboNET [https://wwwn.cdc.gov/arbonet/maps/ADB\_Diseases\_Map/index.html][1]. Genomic data is available online at Genbank, accession numbers [OQ511733][2]-[OQ511812][3]. Mosquito data is available upon reasonable request to authors. Other data is available at [1]: https://wwwn.cdc.gov/arbonet/maps/ADB_Diseases_Map/index.html [2]: /lookup/external-ref?link_type=GEN&access_num=OQ511733&atom=%2Fmedrxiv%2Fearly%2F2023%2F03%2F06%2F2023.03.06.23286851.atom [3]: /lookup/external-ref?link_type=GEN&access_num=OQ511812&atom=%2Fmedrxiv%2Fearly%2F2023%2F03%2F06%2F2023.03.06.23286851.atom