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Boehm AB, Wadford DA, Hughes B, Duong D, Chen A, Padilla T, Wright C, Moua L, Bullick T, Salas M, Morales C, White BJ, Glaser CA, Vugia DJ, Yu AT, Wolfe MK. Trends of Enterovirus D68 Concentrations in Wastewater, California, USA, February 2021-April 2023. Emerg Infect Dis 2023; 29:2362-2365. [PMID: 37877593 PMCID: PMC10617337 DOI: 10.3201/eid2911.231080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
In this retrospective study, we measured enterovirus D68 (EV-D68) genomic RNA in wastewater solids longitudinally at 2 California, USA, wastewater treatment plants twice per week for 26 months. EV-D68 RNA was undetectable except when concentrations increased from mid-July to mid-December 2022, which coincided with a peak in confirmed EV-D68 cases.
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Affiliation(s)
| | | | - Bridgette Hughes
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Dorothea Duong
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Alice Chen
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Tasha Padilla
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Chelsea Wright
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Lisa Moua
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Teal Bullick
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Maria Salas
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Christina Morales
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Bradley J. White
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Carol A. Glaser
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Duc J. Vugia
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Alexander T. Yu
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
| | - Marlene K. Wolfe
- Stanford University, Stanford, California, USA (A.B. Boehm)
- California Department of Public Health, Richmond, California, USA (D.A. Wadford, A. Chen, T. Padilla, C. Wright, L. Moua, T. Bullick, M. Salas, C. Morales, C.A. Glaser, D.J. Vugia, A.T. Yu)
- Verily Life Sciences, South San Francisco, California, USA (B. Hughes, D. Duong, B.J. White)
- Emory University Rollins School of Public Health, Atlanta, Georgia, USA (M.K. Wolfe)
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Skarbinski J, Nugent JR, Wood MS, Liu L, Bullick T, Schapiro JM, Arunleung P, Morales C, Amsden LB, Hsiao CA, Wadford DA, Chai SJ, Reingold A, Wyman SK. Severe Acute Respiratory Syndrome Coronavirus 2 Delta Variant Genomic Variation Associated With Breakthrough Infection in Northern California: A Retrospective Cohort Study. J Infect Dis 2023; 228:878-888. [PMID: 37195913 PMCID: PMC11009495 DOI: 10.1093/infdis/jiad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND The association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic variation and breakthrough infection is not well defined among persons with Delta variant SARS-CoV-2 infection. METHODS In a retrospective cohort, we assessed whether individual nonlineage defining mutations and overall genomic variation (including low-frequency alleles) were associated with breakthrough infection, defined as SARS-CoV-2 infection after coronavirus disease 2019 primary vaccine series. We identified all nonsynonymous single-nucleotide polymorphisms, insertions, and deletions in SARS-CoV-2 genomes with ≥5% allelic frequency and population frequency of ≥5% and ≤95%. Using Poisson regression, we assessed the association with breakthrough infection for each individual mutation and a viral genomic risk score. RESULTS Thirty-six mutations met our inclusion criteria. Among 12 744 persons infected with Delta variant SARS-CoV-2, 5949 (47%) were vaccinated and 6795 (53%) were unvaccinated. Viruses with a viral genomic risk score in the highest quintile were 9% more likely to be associated with breakthrough infection than viruses in the lowest quintile, but including the risk score improved overall predictive model performance (measured by C statistic) by only +0.0006. CONCLUSIONS Genomic variation within SARS-CoV-2 Delta variant was weakly associated with breakthrough infection, but several potential nonlineage defining mutations were identified that might contribute to immune evasion by SARS-CoV-2.
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Affiliation(s)
- Jacek Skarbinski
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
- Department of Infectious Diseases, Oakland Medical Center, Kaiser Permanente Northern California, Oakland, California, USA
- Physician Researcher Program, Kaiser Permanente Northern California, Oakland, California, USA
- The Permanente Medical Group, Kaiser Permanente Northern California, Oakland, California, USA
| | - Joshua R Nugent
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Mariah S Wood
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Liyan Liu
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Teal Bullick
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, USA
| | - Jeffrey M Schapiro
- The Permanente Medical Group, Kaiser Permanente Northern California, Oakland, California, USA
| | - Phacharee Arunleung
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, USA
| | - Christina Morales
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, USA
| | - Laura B Amsden
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Crystal A Hsiao
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, USA
| | - Shua J Chai
- Career Epidemiology Field Officer, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Arthur Reingold
- School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
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Danforth ME, Snyder RE, Feiszli T, Bullick T, Messenger S, Hanson C, Padgett K, Coffey LL, Barker CM, Reisen WK, Kramer VL. Epidemiologic and environmental characterization of the Re-emergence of St. Louis Encephalitis Virus in California, 2015–2020. PLoS Negl Trop Dis 2022; 16:e0010664. [PMID: 35939506 PMCID: PMC9387929 DOI: 10.1371/journal.pntd.0010664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/18/2022] [Accepted: 07/15/2022] [Indexed: 11/18/2022] Open
Abstract
St. Louis encephalitis virus (SLEV) is an endemic flavivirus in the western and southeastern United States, including California. From 1938 to 2003, the virus was detected annually in California, but after West Nile virus (WNV) arrived in 2003, SLEV was not detected again until it re-emerged in Riverside County in 2015. The re-emerging virus in California and other areas of the western US is SLEV genotype III, which previously had been detected only in Argentina, suggesting a South American origin. This study describes SLEV activity in California since its re-emergence in 2015 and compares it to WNV activity during the same period. From 2015 to 2020, SLEV was detected in 1,650 mosquito pools and 26 sentinel chickens, whereas WNV was detected concurrently in 18,108 mosquito pools and 1,542 sentinel chickens from the same samples. There were 24 reported human infections of SLEV in 10 California counties, including two fatalities (case fatality rate: 8%), compared to 2,469 reported human infections of WNV from 43 California counties, with 143 fatalities (case fatality rate: 6%). From 2015 through 2020, SLEV was detected in 17 (29%) of California’s 58 counties, while WNV was detected in 54 (93%). Although mosquitoes and sentinel chickens have been tested routinely for arboviruses in California for over fifty years, surveillance has not been uniform throughout the state. Of note, since 2005 there has been a steady decline in the use of sentinel chickens among vector control agencies, potentially contributing to gaps in SLEV surveillance. The incidence of SLEV disease in California may have been underestimated because human surveillance for SLEV relied on an environmental detection to trigger SLEV patient screening and mosquito surveillance effort is spatially variable. In addition, human diagnostic testing usually relies on changes in host antibodies and SLEV infection can be indistinguishable from infection with other flaviviruses such as WNV, which is more prevalent. St. Louis encephalitis virus is a mosquito-borne virus that can cause human disease and is found in California, where it was detected every year from 1938 to 2003. However, after West Nile virus arrived in 2003, St. Louis encephalitis virus was not detected again until 2015, when it re-emerged in Riverside County. From 2015 through 2020, St. Louis encephalitis virus has been detected in mosquito pools and sentinel chicken sera samples in 16 counties and a total of 24 human disease cases have been reported. However, during that same time-period, West Nile virus has been detected in 10 times as many mosquito pools and 60 times as many chicken sera samples across 54 counties and over 2,400 human disease cases have been reported. Although mosquitoes are tested routinely for both viruses, surveillance is not uniform throughout the state, and there has been a steady decline in the use of sentinel chickens. Since St. Louis encephalitis virus patient screening is dependent upon environmental detection, California may be underestimating the incidence of human disease due to this virus.
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Affiliation(s)
- Mary E. Danforth
- California Department of Public Health, Vector-Borne Disease Section, Richmond and Sacramento, California
- * E-mail:
| | - Robert E. Snyder
- California Department of Public Health, Vector-Borne Disease Section, Richmond and Sacramento, California
| | - Tina Feiszli
- California Department of Public Health, Vector-Borne Disease Section, Richmond and Sacramento, California
| | - Teal Bullick
- California Department of Public Health, Viral and Rickettsial Disease Laboratory, Richmond, California
| | - Sharon Messenger
- California Department of Public Health, Viral and Rickettsial Disease Laboratory, Richmond, California
| | - Carl Hanson
- California Department of Public Health, Viral and Rickettsial Disease Laboratory, Richmond, California
| | - Kerry Padgett
- California Department of Public Health, Vector-Borne Disease Section, Richmond and Sacramento, California
| | - Lark L. Coffey
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Christopher M. Barker
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - William K. Reisen
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Vicki L. Kramer
- California Department of Public Health, Vector-Borne Disease Section, Richmond and Sacramento, California
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