Last data update: Jan 27, 2025. (Total: 48650 publications since 2009)
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Seasonal activity patterns of Ixodes scapularis and Ixodes pacificus in the United States
Eisen L . Ticks Tick Borne Dis 2025 16 (1) 102433 Knowledge of seasonal activity patterns of human-biting life stages of tick species serving as vectors of human disease agents provides basic information on when during the year humans are most at risk for tick bites and tick-borne diseases. Although there is a wealth of published information on seasonal activity patterns of Ixodes scapularis and Ixodes pacificus in the United States, a critical review of the literature for these important tick vectors is lacking. The aims of this paper were to: (i) review what is known about the seasonal activity patterns of I. scapularis and I. pacificus in different parts of their geographic ranges in the US, (ii) provide a synthesis of the main findings, and (iii) outline key knowledge gaps and methodological pitfalls that limit our understanding of variability in seasonal activity patterns. Based on ticks collected while questing or from wild animals, the seasonal activity patterns were found to be similar for I. pacificus in the Far West and I. scapularis in the Southeast, with synchronous activity of larvae and nymphs, peaking in spring (April to June) in the Far West and from spring to early summer (April to July) in the Southeast, and continuous activity of adults from fall through winter and spring with peak activity from fall through winter (November/December to March). In the colder climates of the Upper Midwest and Northeast, I. scapularis adults have a bimodal seasonal pattern, with activity peaks in fall (October to November) and spring (April to May). The seasonal activity patterns for immatures differ between the Upper Midwest, synchronous for larvae and nymphs with peak activity in spring and summer (May to August), and the Northeast, where the peak activity of nymphs in spring and early summer (May to July) precedes that of larvae in summer (July to September). Seasonality of human tick encounters also is influenced by changes over the year in the level of outdoor activities in tick habitat. Studies on the seasonality of ticks infesting humans have primarily focused on the coastal Northeast and the Pacific Coast states, with fewer studies in the Southeast, inland parts of the Northeast, and the Upper Midwest. Discrepancies between seasonal patterns for peak tick questing activity and peak human infestation appear to occur primarily for the adult stages of I. scapularis and I. pacificus. Study design and data presentation limitations of the published literature are discussed. Scarcity of data for seasonal activity patterns of I. pacificus outside of California and for I. scapularis from parts of the Southeast, Northeast, and Upper Midwest is a key knowledge gap. In addition to informing the public of when during the year the risk for tick bites is greatest, high-quality studies describing current seasonal activity patterns also will generate the data needed for robust model-based projections of future climate-driven change in the seasonal activity patterns and provide the baseline needed to empirically determine in the future if the projections were accurate. |
Genomic surveillance for SARS-CoV-2 variants: Circulation of Omicron XBB and JN.1 lineages - United States, May 2023-September 2024
Ma KC , Castro J , Lambrou AS , Rose EB , Cook PW , Batra D , Cubenas C , Hughes LJ , MacCannell DR , Mandal P , Mittal N , Sheth M , Smith C , Winn A , Hall AJ , Wentworth DE , Silk BJ , Thornburg NJ , Paden CR . MMWR Morb Mortal Wkly Rep 2024 73 (42) 938-945 ![]() ![]() CDC continues to track the evolution of SARS-CoV-2, including the Omicron variant and its descendants, using national genomic surveillance. This report summarizes U.S. trends in variant proportion estimates during May 2023-September 2024, a period when SARS-CoV-2 lineages primarily comprised descendants of Omicron variants XBB and JN.1. During summer and fall 2023, multiple descendants of XBB with immune escape substitutions emerged and reached >10% prevalence, including EG.5-like lineages by June 24, FL.1.5.1-like lineages by August 5, HV.1 lineage by September 30, and HK.3-like lineages by November 11. In winter 2023, the JN.1 variant emerged in the United States and rapidly attained predominance nationwide, representing a substantial genetic shift (>30 spike protein amino acid differences) from XBB lineages. Descendants of JN.1 subsequently circulated and reached >10% prevalence, including KQ.1-like and KP.2-like lineages by April 13, KP.3 and LB.1-like lineages by May 25, and KP.3.1.1 by July 20. Surges in COVID-19 cases occurred in winter 2024 during the shift to JN.1 predominance, as well as in summer 2023 and 2024 during circulation of multiple XBB and JN.1 descendants, respectively. The ongoing evolution of the Omicron variant highlights the importance of continued genomic surveillance to guide medical countermeasure development, including the selection of antigens for updated COVID-19 vaccines. |
Genomic cluster formation among invasive group A streptococcal infections in the USA: a whole-genome sequencing and population-based surveillance study
Li Y , Rivers J , Mathis S , Li Z , Chochua S , Metcalf BJ , Beall B , McGee L . Lancet Microbe 2024 100927 ![]() ![]() ![]() BACKGROUND: Clusters of invasive group A streptococcal (iGAS) infection, linked to genomically closely related group A streptococcal (GAS) isolates (referred to as genomic clusters), pose public health threats, and are increasingly identified through whole-genome sequencing (WGS) analysis. In this study, we aimed to assess the risk of genomic cluster formation among iGAS cases not already part of existing genomic clusters. METHODS: In this WGS and population-based surveillance study, we analysed iGAS case isolates from the Active Bacterial Core surveillance (ABCs), which is part of the US Centers for Disease Control and Prevention's Emerging Infections Program, in ten US states from Jan 1, 2015, to Dec 31, 2019. We included all residents in ABCs sites with iGAS infections meeting the case definition and excluded non-conforming GAS infections and cases with whole-genome assemblies of the isolate containing fewer than 1·5 million total bases or more than 150 contigs. For iGAS cases we collected basic demographics, underlying conditions, and risk factors for infection from medical records, and for isolates we included emm types, antimicrobial resistance, and presence of virulence-related genes. Two iGAS cases were defined as genomically clustered if their isolates differed by three or less single-nucleotide variants. An iGAS case not clustered with any previous cases at the time of detection, with a minimum trace-back time of 1 year, was defined as being at risk of cluster formation. We monitored each iGAS case at risk for a minimum of 1 year to identify any cluster formation event, defined as the detection of a subsequent iGAS case clustered with the case at risk. We used the Kaplan-Meier method to estimate the cumulative incidence of cluster formation events over time. We used Cox regression to assess associations between features of cases at risk upon detection and subsequent cluster formation. We developed a random survival forest machine-learning model based on a derivation cohort (random selection of 50% of cases at risk) to predict cluster formation risk. This model was validated using a validation cohort consisting of the remaining 50% of cases at risk. FINDINGS: We identified 2764 iGAS cases at risk from 2016 to 2018, of which 656 (24%) formed genomic clusters by the end of 2019. Overall, the cumulative incidence of cluster formation was 0·057 (95% CI 0·048-0·066) at 30 days after detection, 0·12 (0·11-0·13) at 90 days after detection, and 0·16 (0·15-0·18) at 180 days after detection. A higher risk of cluster formation was associated with emm type (adjusted hazard ratio as compared with emm89 was 2·37 [95% CI 1·71-3·30] for emm1, 2·72 [1·82-4·06] for emm3, 2·28 [1·49-3·51] for emm6, 1·47 [1·05-2·06] for emm12, and 2·21 [1·38-3·56] for emm92), homelessness (1·42 [1·01-1·99]), injection drug use (2·08 [1·59-2·72]), residence in a long-term care facility (1·78 [1·29-2·45]), and the autumn-winter season (1·34 [1·14-1·57]) in multivariable Cox regression analysis. The machine-learning model stratified the validation cohort (n=1382) into groups at low (n=370), moderate (n=738), and high (n=274) risk. The 90-day risk of cluster formation was 0·03 (95% CI 0·01-0·05) for the group at low risk, 0·10 (0·08-0·13) for the group at moderate risk, and 0·21 (0·17-0·25) for the group at high risk. These results were consistent with the cross-validation outcomes in the derivation cohort. INTERPRETATION: Using population-based surveillance data, we found that pathogen, host, and environment factors of iGAS cases were associated with increased likelihood of subsequent genomic cluster formation. Groups at high risk were consistently identified by a predictive model which could inform prevention strategies, although future work to refine the model, incorporating other potential risk factors such as host contact patterns and immunity to GAS, is needed to improve its predictive performance. FUNDING: Centers for Disease Control and Prevention. |
Modeling the population-level impact of a third dose of MMR vaccine on a mumps outbreak at the University of Iowa
Park SW , Lawal T , Marin M , Marlow MA , Grenfell BT , Masters NB . Proc Natl Acad Sci U S A 2024 121 (43) e2403808121 Mumps outbreaks among fully vaccinated young adults have raised questions about potential waning of immunity over time and need for a third dose of the measles, mumps, rubella (MMR) vaccine. However, there are currently limited data on real-life effectiveness of the third-dose MMR vaccine in preventing mumps. Here, we used a deterministic compartmental model to infer the effectiveness of the third-dose MMR vaccine in preventing mumps cases by analyzing the mumps outbreak that occurred at the University of Iowa between August 24, 2015, and May 13, 2016. The modeling approach further allowed us to evaluate the population-level impact of vaccination by different timing in relation to the start of the outbreak and varied coverage levels, and to account for potential sources of bias in estimating vaccine effectiveness. We found large uncertainty in vaccine effectiveness estimates; however, our models showed that early introduction of a third dose of MMR vaccine during a mumps outbreak can be effective in preventing transmission. School holidays, such as the winter break, likely played important roles in preventing mumps transmission. |
Immune escape and attenuated severity associated with the SARS-CoV-2 BA.2.86/JN.1 lineage
Lewnard JA , Mahale P , Malden D , Hong V , Ackerson BK , Lewin BJ , Link-Gelles R , Feldstein LR , Lipsitch M , Tartof SY . Nat Commun 2024 15 (1) 8550 The SARS-CoV-2 BA.2.86 lineage, and its sublineage JN.1 in particular, achieved widespread transmission in the US during winter 2023-24. However, this surge in infections was not accompanied by COVID-19 hospitalizations and mortality commensurate with prior waves. To understand shifts in COVID-19 epidemiology associated with JN.1 emergence, we compared characteristics and clinical outcomes of time-matched cases infected with BA.2.86 lineages (predominantly representing JN.1) versus co-circulating XBB-derived lineages in December, 2023 and January, 2024. Cases infected with BA.2.86 lineages received greater numbers of COVID-19 vaccine doses, including XBB.1.5-targeted boosters, in comparison to cases infected with XBB-derived lineages. Additionally, cases infected with BA.2.86 lineages experienced greater numbers of documented prior SARS-CoV-2 infections. Cases infected with BA.2.86 lineages also experienced lower risk of progression to severe clinical outcomes requiring emergency department consultations or hospital admission. Sensitivity analyses suggested under-ascertainment of prior infections could not explain this apparent attenuation of severity. Our findings implicate escape from immunity acquired from prior vaccination or infection in the emergence of the JN.1 lineage and suggest infections with this lineage are less likely to experience clinically-severe disease. Monitoring of immune escape and clinical severity in emerging SARS-CoV-2 variants remains a priority to inform responses. |
The role of multiple birth and birth complications in the association between assisted reproductive technology conception and autism diagnosis
Winter AS , Yartel AK , Fountain C , Cheslack-Postava K , Zhang Y , Schieve LA , Kissin DM , Bearman P . Am J Epidemiol 2024 193 (10) 1426-1432 In recent decades, the use of assisted reproductive technology (ART) has increased rapidly. To assess the relationship between ART and autism diagnosis, we linked California birth records from 2000 through 2016 with contemporaneous records from the National ART Surveillance System (NASS) and autism caseload records from California's Department of Developmental Services from 2000 through November 2019. All 95 149 birth records that were successfully linked to a NASS record, indicating an ART birth, were matched 1:1 using propensity scores to non-ART births. We calculated the hazard risk ratio for autism diagnosis and the proportions of the relationship between ART conception and autism diagnosis mediated by multiple birth pregnancy and related birth complications. The hazard risk ratio for autism diagnosis following ART compared with non-ART conception is 1.26 (95% CI, 1.17-1.35). Multiple birth, preterm birth, and cesarean delivery jointly mediate 77.9% of the relationship between ART conception and autism diagnosis. Thus, increased use of single embryo transfer in the United States to reduce multiple births and related birth complications may be a strategy to address the risk of autism diagnosis among ART-conceived children. |
Increased circulation of GII.17 noroviruses, six European countries and the United States, 2023 to 2024
Chhabra P , Wong S , Niendorf S , Lederer I , Vennema H , Faber M , Nisavanh A , Jacobsen S , Williams R , Colgan A , Yandle Z , Garvey P , Al-Hello H , Ambert-Balay K , Barclay L , de Graaf M , Celma C , Breuer J , Vinjé J , Douglas A . Euro Surveill 2024 29 (39) ![]() We report an increase in GII.17 norovirus outbreaks and sporadic infections of acute gastroenteritis in Austria, Germany, France, Ireland, the Netherlands, England and the United States during the 2023/24 season. A decrease in GII.4 coincided with GII.17 prevalence increasing to between 17% and 64% of all GII detections. Overall, 84% of the GII.17 strains clustered closely with strains first reported in Romania in 2021 and two new sub-lineages were identified. Norovirus surveillance and molecular characterisation should be prioritised this winter. |
Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States
Perofsky AC , Huddleston J , Hansen CL , Barnes JR , Rowe T , Xu X , Kondor R , Wentworth DE , Lewis N , Whittaker L , Ermetal B , Harvey R , Galiano M , Daniels RS , McCauley JW , Fujisaki S , Nakamura K , Kishida N , Watanabe S , Hasegawa H , Sullivan SG , Barr IG , Subbarao K , Krammer F , Bedford T , Viboud C . Elife 2024 13 ![]() ![]() ![]() Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here, we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997-2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection ynamics, presumably via heterosubtypic cross-immunity. | Seasonal influenza (flu) viruses cause outbreaks every winter. People infected with influenza typically develop mild respiratory symptoms. But flu infections can cause serious illness in young children, older adults and people with chronic medical conditions. Infected or vaccinated individuals develop some immunity, but the viruses evolve quickly to evade these defenses in a process called antigenic drift. As the viruses change, they can re-infect previously immune people. Scientists update the flu vaccine yearly to keep up with this antigenic drift. The immune system fights flu infections by recognizing two proteins, known as antigens, on the virus’s surface, called hemagglutinin (HA) and neuraminidase (NA). However, mutations in the genes encoding these proteins can make them unrecognizable, letting the virus slip past the immune system. Scientists would like to know how these changes affect the size, severity and timing of annual influenza outbreaks. Perofsky et al. show that tracking genetic changes in HA and NA may help improve flu season predictions. The experiments compared the severity of 22 flu seasons caused by the A(H3N2) subtype in the United States with how much HA and NA had evolved since the previous year. The A(H3N2) subtype experiences the fastest rates of antigenic drift and causes more cases and deaths than other seasonal flu viruses. Genetic changes in HA and NA were a better predictor of A(H3N2) outbreak severity than the blood tests for protective antibodies that epidemiologists traditionally use to track flu evolution. However, the prevalence of another subtype of influenza A circulating in the population, called A(H1N1), was an even better predictor of how severe A(H3N2) outbreaks would be. Perofsky et al. are the first to show that genetic changes in NA contribute to the severity of flu seasons. Previous studies suggested a link between genetic changes in HA and flu season severity, and flu vaccines include the HA protein to help the body recognize new influenza strains. The results suggest that adding the NA protein to flu vaccines may improve their effectiveness. In the future, flu forecasters may want to analyze genetic changes in both NA and HA to make their outbreak predictions. Tracking how much of the A(H1N1) subtype is circulating may also be useful for predicting the severity of A(H3N2) outbreaks. | eng |
Use of COVID-19 vaccines for persons aged ≥6 months: Recommendations of the advisory committee on immunization practices - United States, 2024-2025
Panagiotakopoulos L , Moulia DL , Godfrey M , Link-Gelles R , Roper L , Havers FP , Taylor CA , Stokley S , Talbot HK , Schechter R , Brooks O , Daley MF , Fleming-Dutra KE , Wallace M . MMWR Morb Mortal Wkly Rep 2024 73 (37) 819-824 COVID-19 vaccination provides additional protection against severe COVID-19-associated illness and death. Since September 2023, 2023-2024 Formula monovalent XBB.1-strain COVID-19 vaccines have been recommended for use in the United States for all persons aged ≥6 months. However, SARS-CoV-2 continues to evolve, and since winter 2023-2024, Omicron JN.1 lineage strains of SARS-CoV-2, including the JN.1 strain and the KP.2 strain, have been widely circulating in the United States. Further, COVID-19 vaccine effectiveness is known to wane. On June 27, 2024, the Advisory Committee on Immunization Practices (ACIP) recommended 2024-2025 COVID-19 vaccination with a Food and Drug Administration (FDA)-approved or authorized vaccine for all persons aged ≥6 months. On August 22, 2024, FDA approved the 2024-2025 COVID-19 vaccines by Moderna and Pfizer-BioNTech (based on the KP.2 strain) for use in persons aged ≥12 years and authorized these vaccines for use in children aged 6 months-11 years under Emergency Use Authorization (EUA). On August 30, 2024, FDA authorized 2024-2025 COVID-19 vaccine by Novavax (based on the JN.1 strain) for use in persons aged ≥12 years under EUA. ACIP will continue to evaluate new evidence as it becomes available and will update recommendations as needed. |
COVID-19 mortality in Kentucky by age and race: Simpson's Paradox
Auche S , Holiday C , Winter K , Thoroughman D , Spicer KB . Am J Epidemiol 2024 |
Report from the World Health Organization's immunization and vaccines-related implementation research advisory committee (IVIR-AC) ad hoc meeting, 28 June - 1 July 2024
Lambach P , Silal S , Sbarra AN , Crowcroft NS , Frey K , Ferrari M , Vynnycky E , Metcalf CJE , Winter AK , Zimmerman L , Koh M , Sheel M , Kim SY , Munywoki PK , Portnoy A , Aggarwal R , Farooqui HH , Flasche S , Hogan AB , Leung K , Moss WJ , Wang XY . Vaccine 2024 42 (26) 126307 The World Health Organization's Immunization and Vaccines-related Implementation Research Advisory Committee (IVIR-AC) serves to independently review and evaluate vaccine-related research to maximize the potential impact of vaccination programs. From 28 June - 1 July 2024, IVIR-AC was convened for an ad hoc meeting to discuss new evidence on criteria for rubella vaccine introduction and the risk of congenital rubella syndrome. This report summarizes background information on rubella virus transmission and the burden of congenital rubella syndrome, meeting structure and presentations, proceedings, and recommendations. |
Challenges and approaches to establishing multi-pathogen serosurveillance: Findings from the 2023 serosurveillance summit
Carcelen AC , Kong AC , Takahashi S , Hegde S , Jaenisch T , Chu M , Rochford R , Kostandova N , Gurley ES , Wesolowski A , Azman AS , van der Klis FRM , den Hartog G , Drakeley C , Heaney C , Winter AK , Salje H , Rodriguez-Barraquer I , Leung DT , Njenga SM , Kagucia EW , Jambo KC , Wolter N , Charles RC , Saboyá-Díaz MI , Martin DL , Moss WJ . Am J Trop Med Hyg 2024 ![]() ![]() Multiplex-based serological surveillance is a valuable but underutilized tool to understand gaps in population-level exposure, susceptibility, and immunity to infectious diseases. Assays for which blood samples can be tested for antibodies against several pathogens simultaneously, such as multiplex bead immunoassays, can more efficiently integrate public health surveillance in low- and middle-income countries. On March 7-8, 2023 a group of experts representing research institutions, multilateral organizations, private industry, and country partners met to discuss experiences, identify challenges and solutions, and create a community of practice for integrated, multi-pathogen serosurveillance using multiplex bead assay technologies. Participants were divided into six working groups: 1) supply chain; 2) laboratory assays; 3) seroepidemiology; 4) data analytics; 5) sustainable implementation; and 6) use case scenarios. These working groups discussed experiences, challenges, solutions, and research needs to facilitate integrated, multi-pathogen serosurveillance for public health. Several solutions were proposed to address challenges that cut across working groups. |
Airborne bacteria in institutional and commercial buildings in Korea: Characterization with 16S rRNA gene sequencing and association with environmental conditions
Kim YJ , Lee BG , Shim JE , Lee H , Park JH , Yeo MK . Aerosol Sci Technol 2024 ![]() ![]() Information on microorganisms in indoor air of various institutional and commercial buildings has significant value in a public health management perspective. However, there is a lack of prior research comparing indoor airborne microbiota across different categories of those buildings. We characterized indoor airborne bacteria in 10 buildings (two for each of five categories: train station, parking garage, mart, public library, and daycare center) during summer and winter. The 16S rRNA gene in the bacterial gDNA extracted from samples was quantified using quantitative real-time polymerase chain reaction and sequenced with the Illumina MiSeq™ platform for characterizing community composition. We collected information on temperature, relative humidity, CO2 concentration, and particulate matter (PM) concentrations by particle size (<1 µm, 1–2.5 µm, 2.5–10 µm) indoors. We performed a multivariate regression analysis to identify factors influencing bacterial quantity and Permutational Multivariate Analysis of Variance (PERMANOVA) to determine factors affecting cluster dissimilarity. We found that bacterial concentration was significantly (p-values < 0.05) associated with season and CO2 concentration. The PERMANOVA analyses showed the significant (p-values < 0.05) associations of bacterial cluster dissimilarity with season, building category, and CO2. Our study indicated that the season, and CO2 concentrations may be important factors associated with the indoor airborne bacterial concentration and composition. Building category and usage appeared to significantly influence the bacterial community composition but not the concentration. Our study may provide basic data on bacterial community composition and their concentration that are needed for properly managing microbial exposures in occupants or customers of the studied institutional and commercial buildings. Copyright © 2024 American Association for Aerosol Research. © 2024 American Association for Aerosol Research. |
Syndromic gastrointestinal panel diagnostic tests have changed our understanding of the epidemiology of yersiniosis-Foodborne Diseases Active Surveillance Network, 2010-2021
Ray LC , Payne DC , Rounds J , Trevejo RT , Wilson E , Burzlaff K , Garman KN , Lathrop S , Rissman T , Wymore K , Wozny S , Wilson S , Francois Watkins LK , Bruce BB , Weller DL . Open Forum Infect Dis 2024 11 (6) ofae199 ![]() ![]() BACKGROUND: In the US, yersinosis was understood to predominantly occur in winter and among Black or African American infants and Asian children. Increased use of culture-independent diagnostic tests (CIDTs) has led to marked increases in yersinosis diagnoses. METHODS: We describe differences in the epidemiology of yersiniosis diagnosed by CIDT versus culture in 10 US sites, and identify determinants of health associated with diagnostic method. RESULTS: Annual reported incidence increased from 0.3/100 000 in 2010 to 1.3/100 000 in 2021, particularly among adults ≥18 years, regardless of race and ethnicity, and during summer months. The proportion of CIDT-diagnosed infections increased from 3% in 2012 to 89% in 2021. An ill person's demographic characteristics and location of residence had a significant impact on their odds of being diagnosed by CIDT. CONCLUSIONS: Improved detection due to increased CIDT use has altered our understanding of yersinosis epidemiology, however differential access to CIDTs may still affect our understanding of yersinosis. |
Notes from the field: Anthrax on a sheep farm in winter - Texas, December 2023-January 2024
Thompson JM , Spencer K , Maass M , Rollo S , Beesley CA , Marston CK , Hoffmaster AR , Bower WA , Candela MG , Barr JR , Boyer AE , Weiner ZP , Negrón ME , Swaney E , O'Sullivan B . MMWR Morb Mortal Wkly Rep 2024 73 (22) 517-520 |
Challenges of COVID-19 case forecasting in the US, 2020-2021
Lopez VK , Cramer EY , Pagano R , Drake JM , O'Dea EB , Adee M , Ayer T , Chhatwal J , Dalgic OO , Ladd MA , Linas BP , Mueller PP , Xiao J , Bracher J , Castro Rivadeneira AJ , Gerding A , Gneiting T , Huang Y , Jayawardena D , Kanji AH , Le K , Mühlemann A , Niemi J , Ray EL , Stark A , Wang Y , Wattanachit N , Zorn MW , Pei S , Shaman J , Yamana TK , Tarasewicz SR , Wilson DJ , Baccam S , Gurung H , Stage S , Suchoski B , Gao L , Gu Z , Kim M , Li X , Wang G , Wang L , Wang Y , Yu S , Gardner L , Jindal S , Marshall M , Nixon K , Dent J , Hill AL , Kaminsky J , Lee EC , Lemaitre JC , Lessler J , Smith CP , Truelove S , Kinsey M , Mullany LC , Rainwater-Lovett K , Shin L , Tallaksen K , Wilson S , Karlen D , Castro L , Fairchild G , Michaud I , Osthus D , Bian J , Cao W , Gao Z , Lavista Ferres J , Li C , Liu TY , Xie X , Zhang S , Zheng S , Chinazzi M , Davis JT , Mu K , Pastore YPiontti A , Vespignani A , Xiong X , Walraven R , Chen J , Gu Q , Wang L , Xu P , Zhang W , Zou D , Gibson GC , Sheldon D , Srivastava A , Adiga A , Hurt B , Kaur G , Lewis B , Marathe M , Peddireddy AS , Porebski P , Venkatramanan S , Wang L , Prasad PV , Walker JW , Webber AE , Slayton RB , Biggerstaff M , Reich NG , Johansson MA . PLoS Comput Biol 2024 20 (5) e1011200 During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub (https://covid19forecasthub.org). We evaluated approximately 9.7 million forecasts of weekly state-level COVID-19 cases for predictions 1-4 weeks into the future submitted by 24 teams from August 2020 to December 2021. We assessed coverage of central prediction intervals and weighted interval scores (WIS), adjusting for missing forecasts relative to a baseline forecast, and used a Gaussian generalized estimating equation (GEE) model to evaluate differences in skill across epidemic phases that were defined by the effective reproduction number. Overall, we found high variation in skill across individual models, with ensemble-based forecasts outperforming other approaches. Forecast skill relative to the baseline was generally higher for larger jurisdictions (e.g., states compared to counties). Over time, forecasts generally performed worst in periods of rapid changes in reported cases (either in increasing or decreasing epidemic phases) with 95% prediction interval coverage dropping below 50% during the growth phases of the winter 2020, Delta, and Omicron waves. Ideally, case forecasts could serve as a leading indicator of changes in transmission dynamics. However, while most COVID-19 case forecasts outperformed a naïve baseline model, even the most accurate case forecasts were unreliable in key phases. Further research could improve forecasts of leading indicators, like COVID-19 cases, by leveraging additional real-time data, addressing performance across phases, improving the characterization of forecast confidence, and ensuring that forecasts were coherent across spatial scales. In the meantime, it is critical for forecast users to appreciate current limitations and use a broad set of indicators to inform pandemic-related decision making. |
Health care utilization and clinical management of all-cause and norovirus-associated acute gastroenteritis within a US integrated health care system
Cates J , Mattison CP , Groom H , Donald J , Hall RP , Schmidt MA , Hall AJ , Naleway AL , Mirza SA . Open Forum Infect Dis 2024 11 (4) ofae151 BACKGROUND: Norovirus-associated acute gastroenteritis (AGE) exacts a substantial disease burden, yet the health care utilization for and clinical management of norovirus-associated AGE are not well characterized. METHODS: We describe the health care encounters and therapeutics used for patients with all-cause and norovirus-associated AGE in the Kaiser Permanente Northwest health system from 1 April 2014 through 30 September 2016. Medical encounters for patients with AGE were extracted from electronic health records, and encounters within 30 days of one another were grouped into single episodes. An age-stratified random sample of patients completed surveys and provided stool samples for norovirus testing. RESULTS: In total, 40 348 individuals had 52 509 AGE episodes; 460 (14%) of 3310 participants in the substudy tested positive for norovirus. An overall 35% of all-cause AGE episodes and 29% of norovirus-associated AGE episodes had ≥2 encounters. While 80% of norovirus-associated AGE episodes had at least 1 encounter in the outpatient setting, all levels of the health care system were affected: 10%, 22%, 10%, and 2% of norovirus-associated AGE episodes had at least 1 encounter in virtual, urgent care, emergency department, and inpatient settings, respectively. Corresponding proportions of therapeutic use between norovirus-positive and norovirus-negative episodes were 13% and 10% for intravenous hydration (P = .07), 65% and 50% for oral rehydration (P < .001), 7% and 14% for empiric antibiotic therapy (P < .001), and 33% and 18% for antiemetics (P < .001). CONCLUSIONS: Increased health care utilization and therapeutics are likely needed for norovirus-associated AGE episodes during peak norovirus winter seasons, and these data illustrate that effective norovirus vaccines will likely result in less health care utilization. |
Effect of planned school breaks on student absenteeism due to influenza-like illness in school aged children-Oregon School District, Wisconsin September 2014-June 2019
He C , Norton D , Temte JL , Barlow S , Goss M , Temte E , Bell C , Chen G , Uzicanin A . Influenza Other Respir Viruses 2024 18 (1) e13244 BACKGROUND: School-aged children and school reopening dates have important roles in community influenza transmission. Although many studies evaluated the impact of reactive closures during seasonal and pandemic influenza outbreaks on medically attended influenza in surrounding communities, few assess the impact of planned breaks (i.e., school holidays) that coincide with influenza seasons, while accounting for differences in seasonal peak timing. Here, we analyze the effects of winter and spring breaks on influenza risk in school-aged children, measured by student absenteeism due to influenza-like illness (a-ILI). METHODS: We compared a-ILI counts in the 2-week periods before and after each winter and spring break over five consecutive years in a single school district. We introduced a "pseudo-break" of 9 days' duration between winter and spring break each year when school was still in session to serve as a control. The same analysis was applied to each pseudo-break to support any findings of true impact. RESULTS: We found strong associations between winter and spring breaks and a reduction in influenza risk, with a nearly 50% reduction in a-ILI counts post-break compared with the period before break, and the greatest impact when break coincided with increased local influenza activity while accounting for possible temporal and community risk confounders. CONCLUSIONS: These findings suggest that brief breaks of in-person schooling, such as planned breaks lasting 9-16 calendar days, can effectively reduce influenza in schools and community spread. Additional analyses investigating the impact of well-timed shorter breaks on a-ILI may determine an optimal duration for brief school closures to effectively suppress community transmission of influenza. |
Decrypting seasonal patterns of key pollen taxa in cool temperate Australia: A multi-barcode metabarcoding analysis
Tegart LJ , Gabriele S , Dickinson JL , Green BJ , Barberán A , Marthick JR , Bissett A , Johnston FH , Jones PJ . Environ Res 2023 243 117808 Pollen allergies pose a considerable global public health concern. Allergy risk can vary significantly within plant families, yet some key pollen allergens can only be identified to family level by current optical methods. Pollen information with greater taxonomic resolution is therefore required to best support allergy prevention and self-management. We used environmental DNA (eDNA) metabarcoding to deepen taxonomic insights into the seasonal composition of airborne pollen in cool temperate Australia, a region with high rates of allergic respiratory disease. In Hobart, Tasmania, we collected routine weekly air samples from December 2018 until October 2020 and sequenced the internal transcribed spacer 2 (ITS2) and chloroplastic tRNA-Leucine tRNA-Phenylalanine intergenic spacer (trnL-trnF) regions in order to address the following questions: a) What is the genus-level diversity of known and potential aeroallergens in Hobart, in particular, in the families Poaceae, Cupressaceae and Myrtaceae? b) How do the atmospheric concentrations of these taxa change over time, and c) Does trnL-trnF enhance resolution of biodiversity when used in addition to ITS2? Our results suggest that individuals in the region are exposed to temperate grasses including Poa and Bromus in the peak grass pollen season, however low levels of exposure to the subtropical grass Cynodon may occur in autumn and winter. Within Cupressaceae, both metabarcodes showed that exposure is predominantly to pollen from the introduced genera Cupressus and Juniperus. Only ITS2 detected the native genus, Callitris. Both metabarcodes detected Eucalyptus as the major Myrtaceae genus, with trnL-trnF exhibiting primer bias for this family. These findings help refine our understanding of allergy triggers in Tasmania and highlight the utility of multiple metabarcodes in aerobiome studies. |
Four methods for monitoring SARS-CoV-2 and influenza a virus activity in schools
Temte J , Goss M , Barlow S , O'Connor DH , O'Connor SL , Ramuta MD , Uzicanin A . JAMA Netw Open 2023 6 (12) e2346329 This cross-sectional study describes 4 parallel approaches used simultaneously to monitor influenza A virus and SARS-CoV-2 activity within a Wisconsin school district during the Fall 2022 semester and briefly following winter break. | eng |
Mortality surveillance during Winter Storm Uri, United States - 2021
Hanchey A , Jiva S , Bayleyegn T , Schnall A . Disaster Med Public Health Prep 2023 17 e530 OBJECTIVE: On February 12, 2021, Winter Storm Uri hit the United States. To understand the disaster-related causes and circumstances of death, the Centers for Disease Control and Prevention (CDC) activated media mortality surveillance. METHODS: The team searched the internet daily for key terms related to Uri and compiled the information into a standardized media mortality surveillance database to conduct descriptive statistics. RESULTS: Between February 12 and March 2, 2021, the accessed media reported 136 Uri-related deaths from nine states. Most decedents were male (39%) and adults (62.5%). Exposure to extreme temperatures (47.1%) was the most common cause of death. Among indirect deaths, motor vehicle collision (12.5%), and carbon monoxide poisoning (7.4%) represented the top two circumstances. CONCLUSION: This was the first time CDC activated media mortality surveillance for a winter storm. Media mortality surveillance is useful in assessing the impact of a disaster and provides timely data for an all-hazards response approach. |
Use of respiratory syncytial virus vaccines in adults aged ≥60 years: updated recommendations of the Advisory Committee on Immunization Practices - United States, 2024
Britton A , Roper LE , Kotton CN , Hutton DW , Fleming-Dutra KE , Godfrey M , Ortega-Sanchez IR , Broder KR , Talbot HK , Long SS , Havers FP , Melgar M . MMWR Morb Mortal Wkly Rep 2024 73 (32) 696-702 Respiratory syncytial virus (RSV) is a major cause of respiratory illness and hospitalization in older adults during fall and winter in the United States. The 2023-2024 RSV season was the first during which RSV vaccination was recommended for U.S. adults aged ≥60 years, using shared clinical decision-making. On June 26, 2024, the Advisory Committee on Immunization Practices voted to update this recommendation as follows: a single dose of any Food and Drug Administration-approved RSV vaccine (Arexvy [GSK]; Abrysvo [Pfizer]; or mResvia [Moderna]) is now recommended for all adults aged ≥75 years and for adults aged 60-74 years who are at increased risk for severe RSV disease. Adults who have previously received RSV vaccine should not receive another dose. This report summarizes the evidence considered for these updated recommendations, including postlicensure data on vaccine effectiveness and safety, and provides clinical guidance for the use of RSV vaccines in adults aged ≥60 years. These updated recommendations are intended to maximize RSV vaccination coverage among persons most likely to benefit, by clarifying who is at highest risk and by reducing implementation barriers associated with the previous shared clinical decision-making recommendation. Continued postlicensure monitoring will guide future recommendations. |
Long COVID and significant activity limitation among adults, by age - United States, June 1-13, 2022, to June 7-19, 2023
Ford ND , Slaughter D , Edwards D , Dalton A , Perrine C , Vahratian A , Saydah S . MMWR Morb Mortal Wkly Rep 2023 72 (32) 866-870 Long COVID is a condition encompassing a wide range of health problems that emerge, persist, or return following COVID-19. CDC analyzed national repeat cross-sectional Household Pulse Survey data to estimate the prevalence of long COVID and significant related activity limitation among U.S. adults aged ≥18 years by age group. Data from surveys completed between June 1-13, 2022, and June 7-19, 2023, indicated that long COVID prevalence decreased from 7.5% (95% CI = 7.1-7.9) to 6.0% (95% CI = 5.7-6.3) among the overall U.S. adult population, irrespective of history of previous COVID-19, and from 18.9% (95% CI = 17.9-19.8) to 11.0% (95% CI = 10.4-11.6) among U.S. adults reporting previous COVID-19. Among both groups, prevalence decreased from June 1-13, 2022, through January 4-16, 2023, before stabilizing. When stratified by age, only adults aged <60 years experienced significant rates of decline (p<0.01). Among adults reporting previous COVID-19, prevalence decreased among those aged 30-79 years through fall or winter and then stabilized. During June 7-19, 2023, 26.4% (95% CI = 24.0-28.9) of adults with long COVID reported significant activity limitation, the prevalence of which did not change over time. These findings help guide the ongoing COVID-19 prevention efforts and planning for long COVID symptom management and future health care service needs. |
Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments (preprint)
Zulli A , Pan A , Bart SM , Crawford FW , Kaplan EH , Cartter M , Ko AI , Cozens D , Sanchez M , Brackney DE , Peccia J . medRxiv 2021 2021.04.27.21256140 We assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1,000 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samples were analyzed for SARS-CoV-2 RNA concentrations during a six-month time period that overlapped with fall 2020 and winter 2021 COVID-19 outbreaks in each municipality. We fit a single regression model to estimate reported case rates in the six municipalities from SARS-CoV-2 RNA concentrations collected daily from corresponding wastewater treatment facilities. Results demonstrate the ability of SARS-CoV-2 RNA concentrations in primary sludge to estimate COVID-19 reported case rates across treatment facilities and wastewater catchments, with coverage probabilities ranging from 0.94 to 0.96. Leave-one-out cross validation suggests that the model can be broadly applied to wastewater catchments that range in more than one order of magnitude in population served. Estimation of case rates from wastewater data can be useful in locations with limited testing availability or testing disparities, or delays in individual COVID-19 testing programs.Competing Interest StatementThe authors have declared no competing interest.Clinical TrialThis work did not result from a clinical trial. It is a comparison of wastewater concentrations with COVID-19 cases. The COVID-19 cases were obtained from publically available data. No human subjects were involved and all data is de-identified before being publically reported.Funding StatementThis project was supported by Cooperative Agreement no. 6NU50CK000524-01 from the Centers for Disease Control and Prevention using funds from the COVID-19 Paycheck Protection Program and Health Care Enhancement Act Response Activities. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy. See e.g., 45 C.F.R. part 46.102(l)(2), 21 C.F.R. part 56; 42 U.S.C. 241(d); 5 U.S.C. 552a; 44 U.S.C. 3501 et seq. The findings and conclusions of this report are those of the author(s) and do not necessarily represent the official position of the Centers for Disease Control and Prevention.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:No IRB is required. The study used publically available COVID-19 cased data. All data is de-identified.All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI 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).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesCOVID-19 case rate data was obtained from the CT department of health. Plots containing the case rate data and SARS-CoV-2 wastewater concentrations are available at: https://yalecovidwastewater.com/https://yalecovidwastewater.com/ |
COVID-19 cases and hospitalizations averted by case investigation and contact tracing in the United States (preprint)
Rainisch G , Jeon S , Pappas D , Spencer KD , Fischer LS , Adhikari BB , Taylor MM , Greening B , Moonan PK , Oeltmann JE , Kahn EB , Washington ML , Meltzer MI . medRxiv 2021 21 Importance: Evidence of the impact of COVID-19 Case Investigation and Contact Tracing (CICT) programs is lacking. Policymakers need this evidence to assess its value. Objective(s): Estimate COVID-19 cases and hospitalizations averted nationwide by US states' CICT programs. Design(s): We combined data from US CICT programs (e.g., proportion of cases interviewed, contacts notified or monitored, and days to case and contact notification) with incidence data to model CICT impacts over 60 days period (November 25, 2020 to January 23, 2021) during the height of the pandemic. We estimated a range of impacts by varying assumed compliance with isolation and quarantine recommendations. Setting(s): US States and Territories Participants: Fifty-nine state and territorial health departments that received federal funding supporting COVID-19 pandemic response activities were eligible for inclusion. Of these, 22 states and 1 territory reported all measures necessary for the analysis. These 23 jurisdictions covered 42.5% of the US population (140 million persons), spanned all 4 census regions, and reported data that reflected all 59 federally funded CICT programs. Intervention(s): Public health case investigation and contact tracing Main Outcomes and Measures: Cases and hospitalizations averted; percent of cases averted among cases not prevented by vaccination and other non-pharmaceutical interventions (other NPIs). Result(s): We estimated 1.11 million cases and 27,231 hospitalizations were averted by CICT programs under a scenario where 80% of interviewed cases and monitored contacts, and 30% of notified contacts fully complied with isolation and quarantine guidance, eliminating their contributions to future transmission. As many as 1.36 million cases and 33,527 hospitalizations could have been prevented if all interviewed cases and monitored contacts had entered into and fully complied with isolation and quarantine guidelines upon being interviewed or notified. Across all scenarios and jurisdictions, CICT averted a median of 21.2% (range: 1.3% - 65.8%) of the cases not prevented by vaccination and other NPIs. Conclusions and Relevance: CICT programs likely had a substantial role in curtailing the pandemic in most jurisdictions during the winter 2020-2021 peak. Differences in impact across jurisdictions indicate an opportunity to further improve CICT effectiveness. These estimates demonstrate the potential benefits from sustaining and improving these programs. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. |
Respiratory Virus Circulation during the First Year of the COVID-19 Pandemic in the Household Influenza Vaccine Evaluation (HIVE) Cohort (preprint)
Fine SR , Bazzi LA , Callear AP , Petrie JG , Malosh RE , Tucker JE , Smith M , Ibiebele J , McDermott A , Rolfes MA , Monto AS , Martin ET . medRxiv 2022 09 Background The annual reappearance of respiratory viruses has been recognized for decades. The onset of the COVID-19 pandemic altered typical respiratory virus transmission patterns. COVID-19 mitigation measures taken during the pandemic were targeted at SARS-CoV-2 respiratory transmission and thus broadly impacted the burden of acute respiratory illnesses (ARIs), in general. Methods We used the longitudinal Household Influenza Vaccine Evaluation (HIVE) cohort of households in southeast Michigan to characterize mitigation strategy adherence, respiratory illness burden, and the circulation of 15 respiratory viruses during the COVID-19 pandemic determined by RT-PCR of respiratory specimens collected at illness onset. Study participants were surveyed twice during the study period (March 1, 2020, to June 30, 2021), and serologic specimens were collected for antibody measurement by electrochemiluminescence immunoassay. Incidence rates of ARI reports and virus detections were calculated and compared using incidence rate ratios for the study period and a pre-pandemic period of similar length. Results Overall, 437 participants reported a total of 772 ARIs and 329 specimens (42.6%) had respiratory viruses detected. Rhinoviruses were the most frequently detected organism, but seasonal coronaviruses-excluding SARS-CoV-2-were also common. Illness reports and percent positivity were lowest from May to August 2020, when mitigation measures were most stringent. Study participants were more adherent to mitigation measures in the first survey compared with the second survey. Supplemental serology surveillance identified 5.3% seropositivity for SARS-CoV-2 in summer 2020; 3.0% between fall 2020 and winter 2021; and 11.3% in spring 2021. Compared to a pre-pandemic period of similar length, the incidence rate of total reported ARIs for the study period was 50% lower (95% CI: 0.5, 0.6; p<0.001) than the incidence rate from March 1, 2016, to June 30, 2017. Conclusions The burden of ARI in the HIVE cohort during the COVID-19 pandemic fluctuated, with declines occurring concurrently with the widespread use of public health measures. It is notable, however, that rhinovirus and seasonal coronaviruses continued to circulate even as influenza and SARSCoV-2 circulation was low. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. |
Modifications to student quarantine policies in K-12 schools implementing multiple COVID-19 prevention strategies restores in-person education without increasing SARS-CoV-2 transmission risk, January-March 2021 (preprint)
Dawson P , Worrell MC , Malone S , Fritz SA , McLaughlin HP , Montgomery BK , Boyle M , Gomel A , Hayes S , Maricque B , Lai AM , Neidich JA , Tinker SC , Lee JS , Tong S , Orscheln RC , Charney R , Rebmann T , Mooney J , Rains C , Yoon N , Petit M , Towns K , Goddard C , Schmidt S , Barrios LC , Neatherlin JC , Salzer JS , Newland JG . medRxiv 2022 21 Objective: To determine whether modified K-12 student quarantine policies that allow some students to continue in-person education during their quarantine period increase schoolwide SARS-CoV-2 transmission risk following the increase in cases in winter 2020-2021. Method(s): We conducted a prospective cohort study of COVID-19 cases and exposures among students and staff (n=65,621) in 103 Missouri public schools. Participants were offered free, saliva-based RT-PCR testing. An adjusted Cox regression model compared hazard rates of school-based SARS-CoV-2 infections between schools with a modified versus standard quarantine policy. Result(s): From January-March 2021, a projected 23 (1%) school-based transmission events occurred among 1,636 school close contacts. There was no difference in the adjusted hazard rates of school-based SARS-CoV-2 infections between schools with a modified versus standard quarantine policy (hazard ratio=1.00; 95% confidence interval: 0.97-1.03). Discussion(s): School-based SARS-CoV-2 transmission was rare in 103 K-12 schools implementing multiple COVID-19 prevention strategies. Modified student quarantine policies were not associated with increased school incidence of COVID-19. Modifications to student quarantine policies may be a useful strategy for K-12 schools to safely reduce disruptions to in-person education during times of increased COVID-19 community incidence. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Notes from the field: Update on pediatric intracranial infections - 19 states and the District of Columbia, January 2016-March 2023
Accorsi EK , Hall M , Hersh AL , Shah SS , Schrag SJ , Cohen AL . MMWR Morb Mortal Wkly Rep 2023 72 (22) 608-610 In May 2022, CDC began an investigation of a possible increase in pediatric intracranial infections, particularly those caused by Streptococcus bacteria, during the preceding year (1). January 2016–May 2022 data from a large, geographically diverse network of children's hospitals showed altered patterns in pediatric intracranial infections after the onset of the COVID-19 pandemic (1). In this update, extended hospitalization data through March 2023 from 37 hospitals in 19 states and the District of Columbia showed a higher-than-expected number of pediatric intracranial infections beginning in August 2021, with a large peak during winter 2022–2023. Pediatric intracranial infections are recognized as a severe complication of viral respiratory infection and sinusitis (2), and the winter 2022–2023 peak coincided with spikes in respiratory virus circulation*,† (3,4). Even during this peak, intracranial infections remained rare. CDC continues to track trends in pediatric intracranial infections and recommends that all persons aged ≤18 years remain current with recommended vaccinations, including influenza and COVID-19.§ |
Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments
Zulli A , Pan A , Bart SM , Crawford FW , Kaplan EH , Cartter M , Ko AI , Sanchez M , Brown C , Cozens D , Brackney DE , Peccia J . FEMS Microbes 2021 2 xtab022 We assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1700 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samples were analyzed for SARS-CoV-2 RNA concentrations during a 10 month time period that overlapped with October 2020 and winter/spring 2021 COVID-19 outbreaks in each municipality. We fit lagged regression models to estimate reported case rates in the six municipalities from SARS-CoV-2 RNA concentrations collected daily from corresponding wastewater treatment facilities. Results demonstrate the ability of SARS-CoV-2 RNA concentrations in primary sludge to estimate COVID-19 reported case rates across treatment facilities and wastewater catchments, with coverage probabilities ranging from 0.94 to 0.96. Lags of 0 to 1 days resulted in the greatest predictive power for the model. Leave-one-out cross validation suggests that the model can be broadly applied to wastewater catchments that range in more than one order of magnitude in population served. The close relationship between case rates and SARS-CoV-2 concentrations demonstrates the utility of using primary sludge samples for monitoring COVID-19 outbreak dynamics. Estimating case rates from wastewater data can be useful in locations with limited testing availability, testing disparities, or delays in individual COVID-19 testing programs. |
COVID-19 Stats: COVID-19* and Influenza
Gates A , Dias T , van Santen KL , Sheppard M . MMWR Morb Mortal Wkly Rep 2021 70 (15) 573 In late June 2020, the percentage of ED visits for COVID-19 increased and reached a peak of 2.8% of all ED visits in early July before declining through August. This decline was followed by a larger and more prolonged increase beginning in September 2020 that reached a peak (7.2%) in early January 2021. Influenza activity generally begins in October with increased activity throughout the winter months. By the beginning of February 2018, the percentage of ED visits for influenza reached 3.1%, and by the beginning of February 2019, reached 5.0%. During June 2020–March 2021, ED visits for influenza accounted for less than 0.1% of all visits. |
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