29 results on '"Talia M Quandelacy"'
Search Results
2. Reduced spread of influenza and other respiratory viral infections during the COVID-19 pandemic in southern Puerto Rico.
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Talia M Quandelacy, Laura E Adams, Jorge Munoz, Gilberto A Santiago, Sarah Kada, Michael A Johansson, Luisa I Alvarado, Vanessa Rivera-Amill, and Gabriela Paz-Bailey
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Medicine ,Science - Abstract
IntroductionImpacts of COVID-19 mitigation measures on seasonal respiratory viruses is unknown in sub-tropical climates.MethodsWe compared weekly testing and test-positivity of respiratory infections in the 2019-2020 respiratory season to the 2012-2018 seasons in southern Puerto Rico using Wilcoxon signed rank tests.ResultsCompared to the average for the 2012-2018 seasons, test-positivity was significantly lower for Influenza A (pConclusionsMitigation measures and behavioral social distancing choices may have reduced respiratory viral spread in southern Puerto Rico.
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- 2022
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3. Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines.
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Simon Pollett, Michael A Johansson, Nicholas G Reich, David Brett-Major, Sara Y Del Valle, Srinivasan Venkatramanan, Rachel Lowe, Travis Porco, Irina Maljkovic Berry, Alina Deshpande, Moritz U G Kraemer, David L Blazes, Wirichada Pan-Ngum, Alessandro Vespigiani, Suzanne E Mate, Sheetal P Silal, Sasikiran Kandula, Rachel Sippy, Talia M Quandelacy, Jeffrey J Morgan, Jacob Ball, Lindsay C Morton, Benjamin M Althouse, Julie Pavlin, Wilbert van Panhuis, Steven Riley, Matthew Biggerstaff, Cecile Viboud, Oliver Brady, and Caitlin Rivers
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Medicine - Abstract
BackgroundThe importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research.Methods and findingsWe developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies.ConclusionsThese guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement.
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- 2021
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4. Estimating incidence of infection from diverse data sources: Zika virus in Puerto Rico, 2016.
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Talia M Quandelacy, Jessica M Healy, Bradford Greening, Dania M Rodriguez, Koo-Whang Chung, Matthew J Kuehnert, Brad J Biggerstaff, Emilio Dirlikov, Luis Mier-Y-Teran-Romero, Tyler M Sharp, Stephen Waterman, and Michael A Johansson
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Biology (General) ,QH301-705.5 - Abstract
Emerging epidemics are challenging to track. Only a subset of cases is recognized and reported, as seen with the Zika virus (ZIKV) epidemic where large proportions of infection were asymptomatic. However, multiple imperfect indicators of infection provide an opportunity to estimate the underlying incidence of infection. We developed a modeling approach that integrates a generic Time-series Susceptible-Infected-Recovered epidemic model with assumptions about reporting biases in a Bayesian framework and applied it to the 2016 Zika epidemic in Puerto Rico using three indicators: suspected arboviral cases, suspected Zika-associated Guillain-Barré Syndrome cases, and blood bank data. Using this combination of surveillance data, we estimated the peak of the epidemic occurred during the week of August 15, 2016 (the 33rd week of year), and 120 to 140 (50% credible interval [CrI], 95% CrI: 97 to 170) weekly infections per 10,000 population occurred at the peak. By the end of 2016, we estimated that approximately 890,000 (95% CrI: 660,000 to 1,100,000) individuals were infected in 2016 (26%, 95% CrI: 19% to 33%, of the population infected). Utilizing multiple indicators offers the opportunity for real-time and retrospective situational awareness to support epidemic preparedness and response.
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- 2021
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5. Viral etiology and seasonal trends of pediatric acute febrile illness in southern Puerto Rico; a seven-year review.
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Liliana Sánchez-González, Talia M Quandelacy, Michael Johansson, Brenda Torres-Velásquez, Olga Lorenzi, Mariana Tavarez, Sanet Torres, Luisa I Alvarado, and Gabriela Paz-Bailey
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Medicine ,Science - Abstract
BackgroundAcute febrile illness (AFI) is an important cause for seeking health care among children. Knowledge of the most common etiologic agents of AFI and its seasonality is limited in most tropical regions.Methodology/principal findingsTo describe the viral etiology of AFI in pediatric patients (≤18 years) recruited through a sentinel enhanced dengue surveillance system (SEDSS) in Southern Puerto Rico, we analyzed data for patients enrolled from 2012 to May 2018. To identify seasonal patterns, we applied time-series analyses to monthly arboviral and respiratory infection case data. We calculated coherence and phase differences for paired time-series to quantify the association between each time series. A viral pathogen was found in 47% of the 14,738 patients. Influenza A virus was the most common pathogen detected (26%). The incidence of Zika and dengue virus etiologies increased with age. Arboviral infections peaked between June and September throughout the times-series. Respiratory infections have seasonal peaks occurring in the fall and winter months of each year, though patterns vary by individual respiratory pathogen.Conclusions/significanceDistinct seasonal patterns and differences in relative frequency by age groups seen in this study can guide clinical and laboratory assessment in pediatric patients with AFI in Puerto Rico.
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- 2021
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6. Epidemiologic and spatiotemporal trends of Zika Virus disease during the 2016 epidemic in Puerto Rico.
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Tyler M Sharp, Talia M Quandelacy, Laura E Adams, Jomil Torres Aponte, Matthew J Lozier, Kyle Ryff, Mitchelle Flores, Aidsa Rivera, Gilberto A Santiago, Jorge L Muñoz-Jordán, Luisa I Alvarado, Vanessa Rivera-Amill, Myriam Garcia-Negrón, Stephen H Waterman, Gabriela Paz-Bailey, Michael A Johansson, and Brenda Rivera-Garcia
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Arctic medicine. Tropical medicine ,RC955-962 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundAfter Zika virus (ZIKV) emerged in the Americas, laboratory-based surveillance for arboviral diseases in Puerto Rico was adapted to include ZIKV disease.Methods and findingsSuspected cases of arboviral disease reported to Puerto Rico Department of Health were tested for evidence of infection with Zika, dengue, and chikungunya viruses by RT-PCR and IgM ELISA. To describe spatiotemporal trends among confirmed ZIKV disease cases, we analyzed the relationship between municipality-level socio-demographic, climatic, and spatial factors, and both time to detection of the first ZIKV disease case and the midpoint of the outbreak. During November 2015-December 2016, a total of 71,618 suspected arboviral disease cases were reported, of which 39,717 (55.5%; 1.1 cases per 100 residents) tested positive for ZIKV infection. The epidemic peaked in August 2016, when 71.5% of arboviral disease cases reported weekly tested positive for ZIKV infection. Incidence of ZIKV disease was highest among 20-29-year-olds (1.6 cases per 100 residents), and most (62.3%) cases were female. The most frequently reported symptoms were rash (83.0%), headache (64.6%), and myalgia (63.3%). Few patients were hospitalized (1.2%), and 13 (ConclusionsDuring the ZIKV epidemic in Puerto Rico, 1% of residents were reported to public health authorities and had laboratory evidence of ZIKV disease. Transmission was first detected in urban areas of eastern Puerto Rico, where transmission also peaked earlier. These trends suggest that ZIKV was first introduced to Puerto Rico in the east before disseminating throughout the island.
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- 2020
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7. A systematic review and evaluation of Zika virus forecasting and prediction research during a public health emergency of international concern.
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Pei-Ying Kobres, Jean-Paul Chretien, Michael A Johansson, Jeffrey J Morgan, Pai-Yei Whung, Harshini Mukundan, Sara Y Del Valle, Brett M Forshey, Talia M Quandelacy, Matthew Biggerstaff, Cecile Viboud, and Simon Pollett
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Arctic medicine. Tropical medicine ,RC955-962 ,Public aspects of medicine ,RA1-1270 - Abstract
IntroductionEpidemic forecasting and prediction tools have the potential to provide actionable information in the midst of emerging epidemics. While numerous predictive studies were published during the 2016-2017 Zika Virus (ZIKV) pandemic, it remains unknown how timely, reproducible, and actionable the information produced by these studies was.MethodsTo improve the functional use of mathematical modeling in support of future infectious disease outbreaks, we conducted a systematic review of all ZIKV prediction studies published during the recent ZIKV pandemic using the PRISMA guidelines. Using MEDLINE, EMBASE, and grey literature review, we identified studies that forecasted, predicted, or simulated ecological or epidemiological phenomena related to the Zika pandemic that were published as of March 01, 2017. Eligible studies underwent evaluation of objectives, data sources, methods, timeliness, reproducibility, accessibility, and clarity by independent reviewers.Results2034 studies were identified, of which n = 73 met the eligibility criteria. Spatial spread, R0 (basic reproductive number), and epidemic dynamics were most commonly predicted, with few studies predicting Guillain-Barré Syndrome burden (4%), sexual transmission risk (4%), and intervention impact (4%). Most studies specifically examined populations in the Americas (52%), with few African-specific studies (4%). Case count (67%), vector (41%), and demographic data (37%) were the most common data sources. Real-time internet data and pathogen genomic information were used in 7% and 0% of studies, respectively, and social science and behavioral data were typically absent in modeling efforts. Deterministic models were favored over stochastic approaches. Forty percent of studies made model data entirely available, 29% provided all relevant model code, 43% presented uncertainty in all predictions, and 54% provided sufficient methodological detail to allow complete reproducibility. Fifty-one percent of predictions were published after the epidemic peak in the Americas. While the use of preprints improved the accessibility of ZIKV predictions by a median of 119 days sooner than journal publication dates, they were used in only 30% of studies.ConclusionsMany ZIKV predictions were published during the 2016-2017 pandemic. The accessibility, reproducibility, timeliness, and incorporation of uncertainty in these published predictions varied and indicates there is substantial room for improvement. To enhance the utility of analytical tools for outbreak response it is essential to improve the sharing of model data, code, and preprints for future outbreaks, epidemics, and pandemics.
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- 2019
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8. Household Transmission Dynamics of Seasonal Human Coronaviruses
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Talia M Quandelacy, Matt D T Hitchings, Justin Lessler, Jonathan M Read, Charles Vukotich, Andrew S Azman, Henrik Salje, Shanta Zimmer, Hongjiang Gao, Yenlik Zheteyeva, Amra Uzicanin, and Derek A T Cummings
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Infectious Diseases ,Immunology and Allergy - Abstract
Background Household transmission studies inform how viruses spread among close contacts, but few characterize household transmission of endemic coronaviruses. Methods We used data collected from 223 households with school-age children participating in weekly disease surveillance over 2 respiratory virus seasons (December 2015 to May 2017), to describe clinical characteristics of endemic human coronaviruses (HCoV-229E, HcoV-HKU1, HcoV-NL63, HcoV-OC43) infections, and community and household transmission probabilities using a chain-binomial model correcting for missing data from untested households. Results Among 947 participants in 223 households, we observed 121 infections during the study, most commonly subtype HCoV-OC43. Higher proportions of infected children ( Conclusions Our study highlights the need for large household studies to inform household transmission, the challenges in estimating household transmission probabilities from asymptomatic individuals, and implications for controlling endemic CoVs.
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- 2022
9. Limitations introduced by a low participation rate of SARS-CoV-2 seroprevalence data
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Olivia Pluss, Harlan Campbell, Laura Pezzi, Ivonne Morales, Yannik Roell, Talia M Quandelacy, Rahul Krishan Arora, Emily Boucher, Molly M Lamb, May Chu, Till Bärnighausen, and Thomas Jaenisch
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Epidemiology ,General Medicine - Abstract
Background There has been a large influx of COVID-19 seroprevalence studies, but comparability between the seroprevalence estimates has been an issue because of heterogeneities in testing platforms and study methodology. One potential source of heterogeneity is the response or participation rate. Methods We conducted a review of participation rates (PR) in SARS-CoV-2 seroprevalence studies collected by SeroTracker and examined their effect on the validity of study conclusions. PR was calculated as the count of participants for whom the investigators had collected a valid sample, divided by the number of people invited to participate in the study. A multivariable beta generalized linear model with logit link was fitted to determine if the PR of international household and community-based seroprevalence studies was associated with the factors of interest, from 1 December 2019 to 10 March 2021. Results We identified 90 papers based on screening and were able to calculate the PR for 35 out of 90 papers (39%), with a median PR of 70% and an interquartile range of 40.92; 61% of the studies did not report PR. Conclusions Many SARS-CoV-2 seroprevalence studies do not report PR. It is unclear what the median PR rate would be had a larger portion not had limitations in reporting. Low participation rates indicate limited representativeness of results. Non-probabilistic sampling frames were associated with higher participation rates but may be less representative. Standardized definitions of participation rate and data reporting necessary for the PR calculations are essential for understanding the representativeness of seroprevalence estimates in the population of interest.
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- 2022
10. Disparities Made Invisible: Gaps in COVID-19 Data for American Indian and Alaska Native Populations
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Alexandra Skinner, Julia Raifman, Elizabeth Ferrara, Will Raderman, and Talia M. Quandelacy
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Health (social science) ,Health Information Management ,Health Policy ,Public Health, Environmental and Occupational Health - Abstract
Complete COVID-19 data for American Indian/Alaska Native (AI/AN) populations are critical to equitable pandemic response.We used the COVID-19 U.S. State Policy database to document gaps in COVID-19 data reporting for AI/AN people.Sixty-four percent of states do not report AI/AN data for at least one COVID-19 health metric: cases, hospitalizations, deaths, or vaccinations.The lack of AI/AN-specific data masks the disproportionate burden of COVID-19 and presents challenges to COVID-19 prevention, policy implementation, and health equity.Public-facing data disaggregated by race may facilitate rapid response COVID-19 research and policymaking to support AI/AN communities.
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- 2022
11. Predicting virologically confirmed influenza using school absences in Allegheny County, Pennsylvania, USA during the 2007‐2015 influenza seasons
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Kyra H. Grantz, Amra Uzicanin, Yenlik Zheteyeva, David Galloway, Charles J. Vukotich, Hongjiang Gao, Shanta M. Zimmer, Justin Lessler, Jonathan M. Read, Talia M. Quandelacy, Derek A. T. Cummings, and Rachel Bieltz
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Pulmonary and Respiratory Medicine ,Multivariate statistics ,Epidemiology ,Human influenza ,Negative binomial distribution ,Mean absolute error ,Influenza, Human ,Medicine ,Humans ,Child ,Schools ,business.industry ,Public Health, Environmental and Occupational Health ,school‐aged children ,Temperature ,virus diseases ,human influenza ,Influenza transmission ,Original Articles ,prediction ,Pennsylvania ,Infectious Diseases ,surveillance ,Original Article ,Seasons ,business ,Demography - Abstract
Background Children are important in community‐level influenza transmission. School‐based monitoring may inform influenza surveillance. Methods We used reported weekly confirmed influenza in Allegheny County during the 2007 and 2010‐2015 influenza seasons using Pennsylvania's Allegheny County Health Department all‐age influenza cases from health facilities, and all‐cause and influenza‐like illness (ILI)‐specific absences from nine county school districts. Negative binomial regression predicted influenza cases using all‐cause and illness‐specific absence rates, calendar week, average weekly temperature, and relative humidity, using four cross‐validations. Results School districts reported 2 184 220 all‐cause absences (2010‐2015). Three one‐season studies reported 19 577 all‐cause and 3012 ILI‐related absences (2007, 2012, 2015). Over seven seasons, 11 946 confirmed influenza cases were reported. Absences improved seasonal model fits and predictions. Multivariate models using elementary school absences outperformed middle and high school models (relative mean absolute error (relMAE) = 0.94, 0.98, 0.99). K‐5 grade‐specific absence models had lowest mean absolute errors (MAE) in cross‐validations. ILI‐specific absences performed marginally better than all‐cause absences in two years, adjusting for other covariates, but markedly worse one year. Conclusions Our findings suggest seasonal models including K‐5th grade absences predict all‐age‐confirmed influenza and may serve as a useful surveillance tool.
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- 2021
12. Using serological measures to estimate influenza incidence in the presence of secular trends in exposure and immuno‐modulation of antibody response
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Jonathan M. Read, Chaoqiang Jiang, Byran Dai, Derek A. T. Cummings, Yi Guan, Steven Riley, Ruiyin Shen, Hongbo Zhu, Bingyi Yang, Talia M. Quandelacy, Kin On Kwok, and Justin Lessler
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Pulmonary and Respiratory Medicine ,Epidemiology ,serology ,030312 virology ,Antibodies, Viral ,Serology ,Cohort Studies ,03 medical and health sciences ,immunodynamics ,Influenza, Human ,Humans ,Medicine ,Seroconversion ,0303 health sciences ,business.industry ,Incidence ,Influenza A Virus, H3N2 Subtype ,Incidence (epidemiology) ,Public Health, Environmental and Occupational Health ,Antibody titer ,Original Articles ,Hemagglutination Inhibition Tests ,Secular variation ,Titer ,Infectious Diseases ,Antibody response ,Influenza Vaccines ,Antibody Formation ,Immunology ,Original Article ,influenza ,business ,Cohort study - Abstract
Background Influenza infection is often measured by a fourfold antibody titer increase over an influenza season (ie seroconversion). However, this approach may fail when influenza seasons are less distinct as it does not account for transient effects from recent infections. Here, we present a method to determine seroconversion for non‐paired sera, adjusting for changes in individuals’ antibody titers to influenza due to the transient impact of recent exposures, varied sampling times, and laboratory processes. Methods We applied our method using data for five H3N2 strains collected from 942 individuals, aged 2‐90 years, during the first two study visits of the Fluscape cohort study (2009‐2012) in Guangzhou, China. Results After adjustment, apparent seroconversion rates for non‐circulating strains decreased while we observed a 20% increase in seroconversion rates to recently circulating strains. When examining seroconversion to the most recently circulating strain (A/Brisbane/20/2007) in our study, participants aged under 18, and over 64 had the highest seroconversion rates compared to other age groups. Conclusions Our results highlight the need for improved methods when using antibody titers as an endpoint in settings where there is no clear influenza “off” season. Methods, like those presented here, that use titers from circulating and non‐circulating strains may be key.
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- 2020
13. Recent influenza activity in tropical Puerto Rico has become synchronized with mainland US
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Sonja J. Olsen, Gabriela Paz–Bailey, Luisa I. Alvarado, Michael A. Johansson, Jorge L. Muñoz-Jordán, Matthew Lozier, Lenee Blanton, Laura Adams, and Talia M. Quandelacy
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Pulmonary and Respiratory Medicine ,trends ,Male ,Fever ,Influenzavirus B ,Epidemiology ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,030312 virology ,World health ,Dengue fever ,03 medical and health sciences ,Tropical climate ,Influenza, Human ,medicine ,Humans ,Enteric virus ,0303 health sciences ,Tropical Climate ,Puerto Rico ,Public Health, Environmental and Occupational Health ,synchrony ,virus diseases ,COVID-19 ,Influenza a ,Original Articles ,medicine.disease ,United States ,Vaccination ,Infectious Diseases ,Geography ,Influenza A virus ,Population Surveillance ,Mainland ,Original Article ,Female ,Seasons ,influenza ,Demography - Abstract
Background We used data from the Sentinel Enhanced Dengue Surveillance System (SEDSS) to describe influenza trends in southern Puerto Rico during 2012‐2018 and compare them to trends in the United States. Methods Patients with fever onset ≤ 7 days presenting were enrolled. Nasal/oropharyngeal swabs were tested for influenza A and B viruses by PCR. Virologic data were obtained from the US World Health Organization (WHO) Collaborating Laboratories System and the National Respiratory and Enteric Virus Surveillance System (NREVSS). We compared influenza A and B infections identified from SEDSS and WHO/NREVSS laboratories reported by US Department of Health and Human Services (HHS) region using time series decomposition methods, and analysed coherence of climate and influenza trends by region. Results Among 23,124 participants, 9% were positive for influenza A and 5% for influenza B. Influenza A and B viruses were identified year‐round, with no clear seasonal patterns from 2012 to 2015 and peaks in December‐January in 2016‐2017 and 2017‐2018 seasons. Influenza seasons in HHS regions were relatively synchronized in recent years with the seasons in Puerto Rico. We observed high coherence between absolute humidity and influenza A and B virus in HHS regions. In Puerto Rico, coherence was much lower in the early years but increased to similar levels to HHS regions by 2017‐2018. Conclusions Influenza seasons in Puerto Rico have recently become synchronized with seasons in US HHS regions. Current US recommendations are for everyone 6 months and older to receive influenza vaccination by the end of October seem appropriate for Puerto Rico.
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- 2020
14. Recommended reporting items for epidemic forecasting and prediction research: the EPIFORGE 2020 guidelines
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Caitlin Rivers, Rachel Lowe, Oliver J. Brady, Michael A. Johansson, Srinivasan Venkatramanan, Travis C. Porco, Moritz U. G. Kraemer, Benjamin M. Althouse, Rachel Sippy, Suzanne E Mate, Steven Riley, Nicholas G. Reich, Alina Deshpande, Matthew Biggerstaff, Willem G. van Panhuis, Irina Maljkovic Berry, Wirichada Pan-Ngum, Talia M. Quandelacy, Cécile Viboud, Sasikiran Kandula, David L. Blazes, Jacob D Ball, David M. Brett-Major, Julie A. Pavlin, Sara Y. Del Valle, Lindsay Morton, Jeff Morgan, Sheetal Silal, Alessandro Vespigiani, Simon Pollett, and University of St Andrews. Statistics
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Reproducibility of results ,Research design ,Biomedical Research ,Medical Journals ,Epidemics/statistics & numerical data ,Epidemiology ,Delphi method ,Population Modeling ,Checklist/methods ,Guidelines and Guidance ,Mathematical and Statistical Techniques ,Medical Conditions ,Electronics Engineering ,RA0421 ,RA0421 Public health. Hygiene. Preventive Medicine ,Medicine and Health Sciences ,Public and Occupational Health ,health care economics and organizations ,COVID-19/epidemiology ,Communicable disease ,Statistics ,General Medicine ,Research Assessment ,Medical research ,Checklist ,Infectious Diseases ,Systematic review ,Research Design ,Physical Sciences ,Comparators ,Research Reporting Guidelines ,Engineering and Technology ,Medicine ,Psychology ,Guidelines as topic/standards ,education ,NDAS ,Guidelines as Topic ,Research and Analysis Methods ,Communicable Diseases ,Infectious Disease Epidemiology ,SDG 3 - Good Health and Well-being ,Biomedical research/methods ,Humans ,Statistical Methods ,Epidemics ,Actuarial science ,Population Biology ,End user ,COVID-19 ,Reproducibility of Results ,Biology and Life Sciences ,Computational Biology ,Communicable diseases/epidemiology ,Guideline ,Forecasting/methods ,Electronics ,Infectious Disease Modeling ,Medical Humanities ,Mathematics ,Forecasting - Abstract
Background The importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research. Methods and findings We developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies. Conclusions These guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement., Simon Pollett and co-workers describe EPIFORGE, a guideline for reporting research on epidemic forecasting.
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- 2021
15. Reduced spread of influenza and other respiratory viral infections during the COVID-19 pandemic in southern Puerto Rico
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Talia M. Quandelacy, Laura E. Adams, Jorge Munoz, Gilberto A. Santiago, Sarah Kada, Michael A. Johansson, Luisa I. Alvarado, Vanessa Rivera-Amill, and Gabriela Paz–Bailey
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Multidisciplinary ,Respiratory Syncytial Virus, Human ,Influenza, Human ,Puerto Rico ,Viruses ,COVID-19 ,Humans ,Pandemics - Abstract
Introduction Impacts of COVID-19 mitigation measures on seasonal respiratory viruses is unknown in sub-tropical climates. Methods We compared weekly testing and test-positivity of respiratory infections in the 2019–2020 respiratory season to the 2012–2018 seasons in southern Puerto Rico using Wilcoxon signed rank tests. Results Compared to the average for the 2012–2018 seasons, test-positivity was significantly lower for Influenza A (p Conclusions Mitigation measures and behavioral social distancing choices may have reduced respiratory viral spread in southern Puerto Rico.
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- 2021
16. Predicting virologically-confirmed influenza using school absences in Allegheny County, Pennsylvania, USA during the 2007-2015 influenza seasons
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Derek A. T. Cummings, Rachel Bieltz, Talia M. Quandelacy, Jonathan M. Read, Hongjiang Gao, Shanta M. Zimmer, Charles J. Vukotich, Yenlik Zheteyeva, Kyra H. Grantz, David Galloway, Amra Uzicanin, and Justin Lessler
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Multivariate statistics ,business.industry ,Mean absolute error ,Negative binomial distribution ,Medicine ,Influenza transmission ,business ,Demography - Abstract
Background Children are important in community-level influenza transmission. School-based monitoring may inform influenza surveillance. Methods We used reported weekly confirmed influenza in Allegheny County during the 2007, and 2010-2015 influenza seasons using Pennsylvania’s Allegheny County Health Department all-age influenza cases from health facilities, and all-cause and influenza-like illness (ILI)-specific absences from nine county school districts. Negative binomial regression predicted influenza cases using all-cause and illness-specific absence rates, calendar week, average weekly temperature and relative humidity, using four cross-validations. Results School districts reported 2,184,220 all-cause absences (2010-2015). Three one-season studies reported 19,577 all-cause and 3,012 ILI-related absences (2007, 2012, 2015). Over seven seasons, 11,946 confirmed influenza cases were reported. Absences improved seasonal model fits and predictions. Multivariate models using elementary school absences outperformed middle and high school models (relative mean absolute error (relMAE)=0.94, 0.98, 0.99). K-5 grade-specific absence models had lowest mean absolute errors (MAE) in cross-validations. ILI-specific absences performed marginally better than all-cause absences in two years, adjusting for other covariates, but markedly worse one year. Conclusions Our findings suggest seasonal models including K-5th grade absences predict all-age confirmed influenza and may serve as a useful surveillance tool.
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- 2021
17. SARS-CoV-2 Transmission From People Without COVID-19 Symptoms
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Sarah Kada, John T. Brooks, Michael A. Johansson, Matthew Biggerstaff, Jay C. Butler, Rachel B. Slayton, Talia M. Quandelacy, Pragati V. Prasad, and Molly C. Steele
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Pediatrics ,medicine.medical_specialty ,Isolation (health care) ,media_common.quotation_subject ,Basic Reproduction Number ,Asymptomatic ,law.invention ,Incubation period ,Decision Support Techniques ,Infectious Disease Incubation Period ,Hygiene ,law ,Medicine ,Humans ,media_common ,business.industry ,SARS-CoV-2 ,COVID-19 ,Correction ,General Medicine ,Online Only ,Transmission (mechanics) ,Carrier State ,Etiology ,Other ,medicine.symptom ,business ,Basic reproduction number - Abstract
Importance Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiology of coronavirus disease 2019 (COVID-19), is readily transmitted person to person. Optimal control of COVID-19 depends on directing resources and health messaging to mitigation efforts that are most likely to prevent transmission, but the relative importance of such measures has been disputed. Objective To assess the proportion of SARS-CoV-2 transmissions in the community that likely occur from persons without symptoms. Design, Setting, and Participants This decision analytical model assessed the relative amount of transmission from presymptomatic, never symptomatic, and symptomatic individuals across a range of scenarios in which the proportion of transmission from people who never develop symptoms (ie, remain asymptomatic) and the infectious period were varied according to published best estimates. For all estimates, data from a meta-analysis was used to set the incubation period at a median of 5 days. The infectious period duration was maintained at 10 days, and peak infectiousness was varied between 3 and 7 days (−2 and +2 days relative to the median incubation period). The overall proportion of SARS-CoV-2 was varied between 0% and 70% to assess a wide range of possible proportions. Main Outcomes and Measures Level of transmission of SARS-CoV-2 from presymptomatic, never symptomatic, and symptomatic individuals. Results The baseline assumptions for the model were that peak infectiousness occurred at the median of symptom onset and that 30% of individuals with infection never develop symptoms and are 75% as infectious as those who do develop symptoms. Combined, these baseline assumptions imply that persons with infection who never develop symptoms may account for approximately 24% of all transmission. In this base case, 59% of all transmission came from asymptomatic transmission, comprising 35% from presymptomatic individuals and 24% from individuals who never develop symptoms. Under a broad range of values for each of these assumptions, at least 50% of new SARS-CoV-2 infections was estimated to have originated from exposure to individuals with infection but without symptoms. Conclusions and Relevance In this decision analytical model of multiple scenarios of proportions of asymptomatic individuals with COVID-19 and infectious periods, transmission from asymptomatic individuals was estimated to account for more than half of all transmissions. In addition to identification and isolation of persons with symptomatic COVID-19, effective control of spread will require reducing the risk of transmission from people with infection who do not have symptoms. These findings suggest that measures such as wearing masks, hand hygiene, social distancing, and strategic testing of people who are not ill will be foundational to slowing the spread of COVID-19 until safe and effective vaccines are available and widely used.
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- 2021
18. Early insights from statistical and mathematical modeling of key epidemiologic parameters of COVID-19
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Jordan W Tappero, Matthew Biggerstaff, Benjamin J. Cowling, Linh Dinh, Michael A. Johansson, Andrew Rambaut, Jonathan A. Polonsky, K Lane Warmbrod, Jessica Y. Wong, Natsuko Imai, Sarah Kada, Talia M. Quandelacy, Ana Pastore y Piontti, Neil M. Ferguson, Alessandro Vespignani, Verity Hill, Oliver Morgan, Huizhi Gao, Zulma M. Cucunubá, Katelijn Vandemaele, Pragati V. Prasad, and Medical Research Council
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Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19 ,Epidemiology ,Psychological intervention ,coronavirus ,lcsh:Medicine ,Disease ,law.invention ,0302 clinical medicine ,law ,1108 Medical Microbiology ,Pandemic ,Medicine ,030212 general & internal medicine ,mathematical modeling ,Online Report ,Infectious Diseases ,Transmission (mechanics) ,Coronavirus Infections ,Serial interval ,severe acute respiratory syndrome coronavirus 2 ,Microbiology (medical) ,Coronavirus disease 2019 (COVID-19) ,030231 tropical medicine ,Pneumonia, Viral ,epidemiological parameters ,World Health Organization ,Microbiology ,Incubation period ,lcsh:Infectious and parasitic diseases ,2019 novel coronavirus disease ,1117 Public Health and Health Services ,03 medical and health sciences ,Betacoronavirus ,Disease severity ,Disease Transmission, Infectious ,Humans ,lcsh:RC109-216 ,viruses ,mathematical modelling ,Pandemics ,Models, Statistical ,business.industry ,SARS-CoV-2 ,lcsh:R ,COVID-19 ,1103 Clinical Sciences ,Models, Theoretical ,zoonoses ,business ,Demography - Abstract
We report key epidemiologic parameter estimates for coronavirus disease identified in peer-reviewed publications, preprint articles, and online reports. Range estimates for incubation period were 1.8-6.9 days, serial interval 4.0-7.5 days, and doubling time 2.3-7.4 days. The effective reproductive number varied widely, with reductions attributable to interventions. Case burden and infection fatality ratios increased with patient age. Implementation of combined interventions could reduce cases and delay epidemic peak up to 1 month. These parameters for transmission, disease severity, and intervention effectiveness are critical for guiding policy decisions. Estimates will likely change as new information becomes available.
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- 2020
19. Viral etiology and seasonal trends of pediatric acute febrile illness in southern Puerto Rico; a seven-year review
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Liliana Sánchez-González, Sanet Torres, Gabriela Paz-Bailey, Brenda Torres-Velasquez, Talia M. Quandelacy, Mariana Tavarez, Olga D. Lorenzi, Luisa I. Alvarado, and Michael A. Johansson
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RNA viruses ,Pediatrics ,Viral Diseases ,Pulmonology ,Dengue virus ,medicine.disease_cause ,Pathology and Laboratory Medicine ,Geographical locations ,Dengue fever ,Dengue ,Medical Conditions ,Influenza A virus ,Prevalence ,Medicine and Health Sciences ,Child ,Viral etiology ,Multidisciplinary ,Zika Virus Infection ,Incidence (epidemiology) ,Incidence ,Respiratory infection ,Febrile illness ,Infectious Diseases ,Medical Microbiology ,Arboviral Infections ,Child, Preschool ,Viral Pathogens ,Viruses ,Medicine ,Seasons ,Pathogens ,Pediatric Infections ,Research Article ,medicine.medical_specialty ,Adolescent ,Fever ,Science ,Microbiology ,Respiratory Disorders ,Influenza, Human ,medicine ,Humans ,Influenza viruses ,Microbial Pathogens ,Caribbean ,Biology and life sciences ,Flaviviruses ,business.industry ,Puerto Rico ,Infant, Newborn ,Organisms ,Infant ,Dengue Virus ,medicine.disease ,Respiratory Infections ,North America ,Etiology ,People and places ,business ,Arboviruses ,Orthomyxoviruses - Abstract
Background Acute febrile illness (AFI) is an important cause for seeking health care among children. Knowledge of the most common etiologic agents of AFI and its seasonality is limited in most tropical regions. Methodology/Principal findings To describe the viral etiology of AFI in pediatric patients (≤18 years) recruited through a sentinel enhanced dengue surveillance system (SEDSS) in Southern Puerto Rico, we analyzed data for patients enrolled from 2012 to May 2018. To identify seasonal patterns, we applied time-series analyses to monthly arboviral and respiratory infection case data. We calculated coherence and phase differences for paired time-series to quantify the association between each time series. A viral pathogen was found in 47% of the 14,738 patients. Influenza A virus was the most common pathogen detected (26%). The incidence of Zika and dengue virus etiologies increased with age. Arboviral infections peaked between June and September throughout the times-series. Respiratory infections have seasonal peaks occurring in the fall and winter months of each year, though patterns vary by individual respiratory pathogen. Conclusions/Significance Distinct seasonal patterns and differences in relative frequency by age groups seen in this study can guide clinical and laboratory assessment in pediatric patients with AFI in Puerto Rico.
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- 2020
20. Author response for 'Recent influenza activity in tropical Puerto Rico has become synchronized with mainland US'
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Michael A. Johansson, Gabriela Paz-Bailey, Talia M. Quandelacy, Jorge L. Muñoz-Jordán, Sonja J. Olsen, Matthew Lozier, Laura Adams, Lenee Blanton, and Luisa I. Alvarado
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Geography ,Ethnology ,Mainland - Published
- 2020
21. Estimating incidence of infection from diverse data sources: Zika virus in Puerto Rico, 2016
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Michael A. Johansson, Luis Mier-y-Teran-Romero, Emilio Dirlikov, Dania M. Rodriguez, Tyler M. Sharp, Brad J. Biggerstaff, Matthew J. Kuehnert, Bradford Greening, Jessica M. Healy, Koo-Whang Chung, Stephen H. Waterman, and Talia M. Quandelacy
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RNA viruses ,Viral Diseases ,Databases, Factual ,Epidemiology ,Autoimmune diseases ,Guillain-Barre syndrome ,Clinical immunology ,Pathology and Laboratory Medicine ,Geographical locations ,Zika virus ,Medical Conditions ,0302 clinical medicine ,Medicine and Health Sciences ,Credible interval ,Public Health Surveillance ,030212 general & internal medicine ,Biology (General) ,education.field_of_study ,Ecology ,biology ,Zika Virus Infection ,Incidence ,Incidence (epidemiology) ,Infectious Diseases ,Computational Theory and Mathematics ,Arboviral Infections ,Medical Microbiology ,Preparedness ,Viral Pathogens ,Modeling and Simulation ,Viruses ,Pathogens ,medicine.symptom ,Research Article ,Neglected Tropical Diseases ,medicine.medical_specialty ,Infectious Disease Control ,QH301-705.5 ,Immunology ,030231 tropical medicine ,Population ,Disease Surveillance ,Microbiology ,Asymptomatic ,Infectious Disease Epidemiology ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Genetics ,medicine ,Humans ,Epidemics ,education ,Microbial Pathogens ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Caribbean ,Models, Statistical ,Biology and life sciences ,Flaviviruses ,business.industry ,Puerto Rico ,Organisms ,Chikungunya Infection ,Computational Biology ,Zika Virus ,Tropical Diseases ,medicine.disease ,biology.organism_classification ,Clinical medicine ,Infectious Disease Surveillance ,North America ,People and places ,Epidemic model ,business ,Blood bank ,Demography - Abstract
Emerging epidemics are challenging to track. Only a subset of cases is recognized and reported, as seen with the Zika virus (ZIKV) epidemic where large proportions of infection were asymptomatic. However, multiple imperfect indicators of infection provide an opportunity to estimate the underlying incidence of infection. We developed a modeling approach that integrates a generic Time-series Susceptible-Infected-Recovered epidemic model with assumptions about reporting biases in a Bayesian framework and applied it to the 2016 Zika epidemic in Puerto Rico using three indicators: suspected arboviral cases, suspected Zika-associated Guillain-Barré Syndrome cases, and blood bank data. Using this combination of surveillance data, we estimated the peak of the epidemic occurred during the week of August 15, 2016 (the 33rd week of year), and 120 to 140 (50% credible interval [CrI], 95% CrI: 97 to 170) weekly infections per 10,000 population occurred at the peak. By the end of 2016, we estimated that approximately 890,000 (95% CrI: 660,000 to 1,100,000) individuals were infected in 2016 (26%, 95% CrI: 19% to 33%, of the population infected). Utilizing multiple indicators offers the opportunity for real-time and retrospective situational awareness to support epidemic preparedness and response., Author summary Zika virus (ZIKV) infections, like many infections, are generally underreported due to asymptomatic, mild, or unrecognized cases. Using available surveillance indicators reflecting imperfect proxies of infection, we developed a modeling approach to estimate the weekly incidence of infection by combining independent surveillance indicators and assumptions about system-specific reporting biases in a Bayesian framework. Using our approach, we estimated that approximately 890,000 people in the population were infected with Zika in Puerto Rico in 2016, much higher than the 36,316 reported confirmed infections. Our framework has broad application to other diseases where cases may be underreported through traditional disease surveillance and can provide near real-time changes in incidences.
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- 2021
22. Epidemiologic and spatiotemporal trends of Zika Virus disease during the 2016 epidemic in Puerto Rico
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Matthew Lozier, Jorge L. Muñoz-Jordán, Talia M. Quandelacy, Aidsa Rivera, Laura Adams, Gilberto A. Santiago, Vanessa Rivera-Amill, Jomil Torres Aponte, Myriam Garcia-Negron, Michael A. Johansson, Brenda Rivera-Garcia, Tyler M. Sharp, Luisa I. Alvarado, Stephen H. Waterman, Mitchelle Flores, Gabriela Paz-Bailey, and Kyle Ryff
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Male ,0301 basic medicine ,Zika virus disease ,RC955-962 ,030231 tropical medicine ,medicine.disease_cause ,Dengue fever ,Zika virus ,03 medical and health sciences ,Spatio-Temporal Analysis ,0302 clinical medicine ,Arctic medicine. Tropical medicine ,medicine ,Humans ,Chikungunya ,Epidemics ,Retrospective Studies ,biology ,Zika Virus Infection ,business.industry ,Transmission (medicine) ,Incidence ,Incidence (epidemiology) ,Puerto Rico ,Hazard ratio ,Public Health, Environmental and Occupational Health ,Outbreak ,Zika Virus ,medicine.disease ,biology.organism_classification ,030104 developmental biology ,Infectious Diseases ,Female ,Public aspects of medicine ,RA1-1270 ,business ,Demography - Abstract
BackgroundAfter Zika virus (ZIKV) emerged in the Americas, laboratory-based surveillance for arboviral diseases in Puerto Rico was adapted to include ZIKV disease.Methods and findingsSuspected cases of arboviral disease reported to Puerto Rico Department of Health were tested for evidence of infection with Zika, dengue, and chikungunya viruses by RT-PCR and IgM ELISA. To describe spatiotemporal trends among confirmed ZIKV disease cases, we analyzed the relationship between municipality-level socio-demographic, climatic, and spatial factors, and both time to detection of the first ZIKV disease case and the midpoint of the outbreak. During November 2015-December 2016, a total of 71,618 suspected arboviral disease cases were reported, of which 39,717 (55.5%; 1.1 cases per 100 residents) tested positive for ZIKV infection. The epidemic peaked in August 2016, when 71.5% of arboviral disease cases reported weekly tested positive for ZIKV infection. Incidence of ZIKV disease was highest among 20-29-year-olds (1.6 cases per 100 residents), and most (62.3%) cases were female. The most frequently reported symptoms were rash (83.0%), headache (64.6%), and myalgia (63.3%). Few patients were hospitalized (1.2%), and 13 (ConclusionsDuring the ZIKV epidemic in Puerto Rico, 1% of residents were reported to public health authorities and had laboratory evidence of ZIKV disease. Transmission was first detected in urban areas of eastern Puerto Rico, where transmission also peaked earlier. These trends suggest that ZIKV was first introduced to Puerto Rico in the east before disseminating throughout the island.
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- 2020
23. Predicting virologically confirmed influenza using school absences in PA
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Justin Lessler, Rachel Bieltz, Hongjiang Gao, David Galloway, Shanta M. Zimmer, Yenlik Zheteyeva, Amra Uzicanin, Talia M. Quandelacy, Derek A. T. Cummings, Chuck Vukotich, and Kyra H. Grantz
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School type ,Gerontology ,Multivariate statistics ,business.industry ,school ,School district ,Standard protocol ,surveillance ,General Earth and Planetary Sciences ,Medicine ,ISDS 2016 Conference Abstracts ,series ,business ,influenza ,time ,General Environmental Science ,Demography - Abstract
Objective To determine if all-cause and cause-specific school absences improve predictions of virologically confirmed influenza in the community. Introduction School-based influenza surveillance has been considered for real-time monitoring of influenza, as children 5-17 years old play an important role in community-level transmission. Methods The Allegheny County Department of Health provided virologically confirmed influenza data collected from all emergency departments and outpatient providers in the county for 2007 and 2011-2016. All-cause school absence rates were collected from nine school districts within Allegheny County for 2010-2015. For a subset of these schools, in addition to all-cause absences, influenza-like illness (ILI)-specific absences were collected using a standard protocol: 10 K-5 schools in one school district (2007-2008), nine K-12 schools in two school districts (2012-2013), and nine K-12 schools from three school districts (2015-2016). We used negative binomial regression to predict weekly county-level influenza cases in Allegheny County, Pennsylvania, during the 2010-2015 influenza seasons. We included the following covariates in candidate models: all-cause school absence rates with different lags (weekly, 1-3 week lags, assessed in separate models using all other covariates) and administrative levels (county, school type, and grade), week and month of the year (assessed in separate models), average weekly temperature, and average weekly relative humidity. Separately, for the three districts for which ILI-specific and all-cause absences were available, we predicted weekly county-level influenza cases using all-cause and ILI-specific absences with all previously stated covariates. We used several cross- validation approaches to assess models, including leave 20% of weeks out, leave 20% of schools out, and leave 52-weeks out. Results Overall, 2,395,020 all-cause absences were observed in nine school districts. From the subset of schools that collected ILI-specific absences, 14,078 all-cause and 2,617 ILI-related absences were reported. A total of 11,946 virologically confirmed influenza cases were reported in Allegheny County (Figure 1). Inclusion of 1-week lagged absence rates in multivariate models improved model fits and predictions of influenza cases over models using week of year and weekly average temperature (change in AIC=-4). Using grade-specific all-cause absences, absences from lower grades explained data best. For example, kindergarten absences explained 22.1% of model deviance compared to 0.43% using 12 th grade absences in validation. Multivariate models of week-lagged kindergarten absences, week of year, and weekly average temperature had the best fits over other grade-specific multivariate models (change in AIC=-6 comparing K to 12 th grade). The utility of ILI-specific absences compared to total absences is mixed, performing marginally better, adjusting for other covariates, in 2 years, but markedly worse in 1 year. However, these results were based on a small number of observations. Conclusions Our findings suggest models including younger student absences improve predictions of virologically confirmed influenza. We found ILI-specific absences performed similarly to all-cause absences; however, more observations are needed to assess the relative performances of these two datasets.
- Published
- 2017
24. A systematic review and evaluation of Zika virus forecasting and prediction research during a public health emergency of international concern
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Pai-Yei Whung, Pei-Ying Kobres, Jean Paul Chretien, Simon Pollett, Brett M. Forshey, Cécile Viboud, Harshini Mukundan, S. Y. Del Valle, Michael A. Johansson, Matthew Biggerstaff, James Morgan, and Talia M. Quandelacy
- Subjects
RNA viruses ,Spatial Epidemiology ,Critical Care and Emergency Medicine ,Databases, Factual ,Epidemiology ,RC955-962 ,Pathology and Laboratory Medicine ,Disease Outbreaks ,Zika virus ,Database and Informatics Methods ,Mathematical and Statistical Techniques ,0302 clinical medicine ,Arctic medicine. Tropical medicine ,Pandemic ,Medicine and Health Sciences ,Public and Occupational Health ,030212 general & internal medicine ,Database Searching ,0303 health sciences ,biology ,Zika Virus Infection ,Statistics ,Spatial epidemiology ,Research Assessment ,Reproducibility ,3. Good health ,Geography ,Infectious Diseases ,Systematic review ,Medical Microbiology ,Viral Pathogens ,Preparedness ,Viruses ,Physical Sciences ,Public Health ,Pathogens ,Public aspects of medicine ,RA1-1270 ,Research Article ,medicine.medical_specialty ,Sexual transmission ,Systematic Reviews ,030231 tropical medicine ,MEDLINE ,Research and Analysis Methods ,Guillain-Barre Syndrome ,Microbiology ,03 medical and health sciences ,Environmental health ,medicine ,Humans ,Statistical Methods ,Microbial Pathogens ,Pandemics ,030304 developmental biology ,Models, Statistical ,Biology and life sciences ,Flaviviruses ,business.industry ,Public health ,Organisms ,Public Health, Environmental and Occupational Health ,Reproducibility of Results ,Outbreak ,Zika Virus ,Models, Theoretical ,biology.organism_classification ,business ,Basic reproduction number ,Mathematics ,Forecasting - Abstract
Introduction Epidemic forecasting and prediction tools have the potential to provide actionable information in the midst of emerging epidemics. While numerous predictive studies were published during the 2016–2017 Zika Virus (ZIKV) pandemic, it remains unknown how timely, reproducible, and actionable the information produced by these studies was. Methods To improve the functional use of mathematical modeling in support of future infectious disease outbreaks, we conducted a systematic review of all ZIKV prediction studies published during the recent ZIKV pandemic using the PRISMA guidelines. Using MEDLINE, EMBASE, and grey literature review, we identified studies that forecasted, predicted, or simulated ecological or epidemiological phenomena related to the Zika pandemic that were published as of March 01, 2017. Eligible studies underwent evaluation of objectives, data sources, methods, timeliness, reproducibility, accessibility, and clarity by independent reviewers. Results 2034 studies were identified, of which n = 73 met the eligibility criteria. Spatial spread, R0 (basic reproductive number), and epidemic dynamics were most commonly predicted, with few studies predicting Guillain-Barré Syndrome burden (4%), sexual transmission risk (4%), and intervention impact (4%). Most studies specifically examined populations in the Americas (52%), with few African-specific studies (4%). Case count (67%), vector (41%), and demographic data (37%) were the most common data sources. Real-time internet data and pathogen genomic information were used in 7% and 0% of studies, respectively, and social science and behavioral data were typically absent in modeling efforts. Deterministic models were favored over stochastic approaches. Forty percent of studies made model data entirely available, 29% provided all relevant model code, 43% presented uncertainty in all predictions, and 54% provided sufficient methodological detail to allow complete reproducibility. Fifty-one percent of predictions were published after the epidemic peak in the Americas. While the use of preprints improved the accessibility of ZIKV predictions by a median of 119 days sooner than journal publication dates, they were used in only 30% of studies. Conclusions Many ZIKV predictions were published during the 2016–2017 pandemic. The accessibility, reproducibility, timeliness, and incorporation of uncertainty in these published predictions varied and indicates there is substantial room for improvement. To enhance the utility of analytical tools for outbreak response it is essential to improve the sharing of model data, code, and preprints for future outbreaks, epidemics, and pandemics., Author summary Researchers published many studies which sought to predict and forecast important features of Zika virus (ZIKV) infections and their spread during the 2016–2017 ZIKV pandemic. We conducted a comprehensive review of such ZIKV prediction studies and evaluated their aims, the data sources they used, which methods were used, how timely they were published, and whether they provided sufficient information to be used or reproduced by others. Of the 73 studies evaluated, we found the accessibility, reproducibility, timeliness, and incorporation of uncertainty in these published predictions varied; indicating there is substantial room for improvement. We identified that the release of study findings before formal journal publication (‘pre-prints’) increased the timeliness of Zika prediction studies, but note they were infrequently used during this public health emergency. Addressing these areas can improve our understanding of Zika and other outbreaks and ensure forecasts can inform preparedness and response to future outbreaks, epidemics, and pandemics.
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- 2019
25. Age- and Sex-related Risk Factors for Influenza-associated Mortality in the United States Between 1997–2007
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Talia M. Quandelacy, Vivek Charu, Edward Goldstein, Marc Lipsitch, and Cécile Viboud
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Adult ,Influenzavirus A ,Male ,Pediatrics ,medicine.medical_specialty ,Adolescent ,Influenzavirus B ,Epidemiology ,Original Contributions ,Disease ,Age and sex ,Young Adult ,Sex Factors ,Risk Factors ,Diabetes mellitus ,Influenza, Human ,medicine ,Humans ,Young adult ,Child ,Aged ,business.industry ,Mortality rate ,Age Factors ,Pneumonia ,Middle Aged ,medicine.disease ,United States ,Confidence interval ,Vaccination ,Female ,business - Abstract
Limited information on age- and sex-specific estimates of influenza-associated death with different underlying causes is currently available. We regressed weekly age- and sex-specific US mortality outcomes underlying several causes between 1997 and 2007 to incidence proxies for influenza A/H3N2, A/H1N1, and B that combine data on influenza-like illness consultations and respiratory specimen testing, adjusting for seasonal baselines and time trends. Adults older than 75 years of age had the highest average annual rate of influenza-associated mortality, with 141.15 deaths per 100,000 people (95% confidence interval (CI): 118.3, 163.9), whereas children under 18 had the lowest average mortality rate, with 0.41 deaths per 100,000 people (95% CI: 0.23, 0.60). In addition to respiratory and circulatory causes, mortality with underlying cancer, diabetes, renal disease, and Alzheimer disease had a contribution from influenza in adult age groups, whereas mortality with underlying septicemia had a contribution from influenza in children. For adults, within several age groups and for several underlying causes, the rate of influenza-associated mortality was somewhat higher in men than in women. Of note, in men 50-64 years of age, our estimate for the average annual rate of influenza-associated cancer mortality per 100,000 persons (1.90, 95% CI: 1.20, 2.62) is similar to the corresponding rate of influenza-associated respiratory deaths (1.81, 95% CI: 1.42, 2.21). Age, sex, and underlying health conditions should be considered when planning influenza vaccination and treatment strategies.
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- 2013
26. The Role of Disease Surveillance in Achieving IHR Compliance by 2012
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Roberta Andraghetti, Ricardo Hora, Talia M. Quandelacy, Matthew C Johns, Joel M. Montgomery, Vito G. Roque, Jean-Baptiste Meynard, and David L. Blazes
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Disease surveillance ,medicine.medical_specialty ,Health (social science) ,business.industry ,Public health ,Public Health, Environmental and Occupational Health ,Capacity building ,General Medicine ,Management, Monitoring, Policy and Law ,Public administration ,International Health Regulations ,Unit (housing) ,Compliance (psychology) ,Environmental health ,Member state ,Medicine ,business ,Human services - Abstract
The World Health Organization's revised International Health Regulations (IHR (2005)) call for member state compliance by mid-2012. Variation in disease surveillance and core public health capacities will affect each member state's ability to meet this deadline. We report on topics presented at the preconference workshop, “The Interaction of Disease Surveillance and the International Health Regulations,” held at the 2010 International Society for Disease Surveillance conference in Park City, Utah. Presenters were from the Pan American Health Organization (PAHO), the U.S. Department of Health and Human Services (HHS), the Centers for Disease Control and Prevention (CDC), the Armed Forces Health Surveillance Center, U.S. Naval Research Unit Six, the Philippines' National Epidemiologic Center, and the French armed forces. The topics addressed were: an overview of the revised IHRs; disease surveillance systems implemented in Peru, the Philippines, and by the French armed forces; the capacity building efforts ...
- Published
- 2011
27. Malaria and other vector-borne infection surveillance in the U.S. Department of Defense Armed Forces Health Surveillance Center-Global Emerging Infections Surveillance program: review of 2009 accomplishments
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Mark M, Fukuda, Terry A, Klein, Tadeusz, Kochel, Talia M, Quandelacy, Bryan L, Smith, Jeff, Villinski, Delia, Bethell, Stuart, Tyner, Youry, Se, Chanthap, Lon, David, Saunders, Jacob, Johnson, Eric, Wagar, Douglas, Walsh, Matthew, Kasper, Jose L, Sanchez, Clara J, Witt, Qin, Cheng, Norman, Waters, Sanjaya K, Shrestha, Julie A, Pavlin, Andres G, Lescano, Paul C F, Graf, Jason H, Richardson, Salomon, Durand, William O, Rogers, David L, Blazes, Kevin L, Russell, Hoseah, Akala, Joel C, Gaydos, Robert F, DeFraites, Panita, Gosi, Ans, Timmermans, Chad, Yasuda, Gary, Brice, Fred, Eyase, Karl, Kronmann, Peter, Sebeny, Robert, Gibbons, Richard, Jarman, John, Waitumbi, David, Schnabel, Allen, Richards, and Dennis, Shanks
- Subjects
Veterinary medicine ,medicine.medical_specialty ,Drug Resistance ,Review ,Global Health ,Communicable Diseases, Emerging ,Military medicine ,Environmental health ,Zoonoses ,Epidemiology ,medicine ,Global health ,Animals ,Humans ,Military Medicine ,business.industry ,Public health ,Public Health, Environmental and Occupational Health ,Arthropod Vectors ,medicine.disease ,United States ,Malaria ,Infectious disease (medical specialty) ,business ,Sentinel Surveillance ,Arthropod Vector ,Tourism - Abstract
Vector-borne infections (VBI) are defined as infectious diseases transmitted by the bite or mechanical transfer of arthropod vectors. They constitute a significant proportion of the global infectious disease burden. United States (U.S.) Department of Defense (DoD) personnel are especially vulnerable to VBIs due to occupational contact with arthropod vectors, immunological naivete to previously unencountered pathogens, and limited diagnostic and treatment options available in the austere and unstable environments sometimes associated with military operations. In addition to the risk uniquely encountered by military populations, other factors have driven the worldwide emergence of VBIs. Unprecedented levels of global travel, tourism and trade, and blurred lines of demarcation between zoonotic VBI reservoirs and human populations increase vector exposure. Urban growth in previously undeveloped regions and perturbations in global weather patterns also contribute to the rise of VBIs. The Armed Forces Health Surveillance Center-Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) and its partners at DoD overseas laboratories form a network to better characterize the nature, emergence and growth of VBIs globally. In 2009 the network tested 19,730 specimens from 25 sites for Plasmodium species and malaria drug resistance phenotypes and nearly another 10,000 samples to determine the etiologies of non-Plasmodium species VBIs from regions spanning from Oceania to Africa, South America, and northeast, south and Southeast Asia. This review describes recent VBI-related epidemiological studies conducted by AFHSC-GEIS partner laboratories within the OCONUS DoD laboratory network emphasizing their impact on human populations.
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- 2011
28. The Role of Disease Surveillance in Achieving IHR Compliance by 2012.
- Author
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Talia M. Quandelacy, Matthew C. Johns, Roberta Andraghetti, Ricardo Hora, Jean-Baptiste Meynard, Joel M. Montgomery, Vito G. Roque, and David L. Blazes
- Abstract
The World Health Organization''s revised International Health Regulations (IHR (2005)) call for member state compliance by mid-2012. Variation in disease surveillance and core public health capacities will affect each member state''s ability to meet this deadline. We report on topics presented at the preconference workshop, “The Interaction of Disease Surveillance and the International Health Regulations,” held at the 2010 International Society for Disease Surveillance conference in Park City, Utah. Presenters were from the Pan American Health Organization (PAHO), the U.S. Department of Health and Human Services (HHS), the Centers for Disease Control and Prevention (CDC), the Armed Forces Health Surveillance Center, U.S. Naval Research Unit Six, the Philippines'' National Epidemiologic Center, and the French armed forces. The topics addressed were: an overview of the revised IHRs; disease surveillance systems implemented in Peru, the Philippines, and by the French armed forces; the capacity building efforts of the CDC; partnerships and contributions to IHR compliance from HHS; and the application of the IHRs to special populations. Results from the meeting evaluation indicate that many participants found the information useful in better understanding current efforts of the U.S. government and international organizations, areas for collaboration, and how the IHRs apply to their countries'' public health systems. Topics to address at future workshops include progress and challenges to IHR implementation across all member states and additional examples of how disease surveillance supports the IHRs in resource-constrained countries. The preconference workshop provided the opportunity to convene public health experts from all regions of the world. Stronger collaborations and support to better detect and respond to public health events through building sustainable disease surveillance systems will not only help member states to meet IHR compliance by 2012, but will also improve pandemic preparedness and global health security. [ABSTRACT FROM AUTHOR]
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- 2011
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29. Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19
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Matthew Biggerstaff, Benjamin J. Cowling, Zulma M. Cucunubá, Linh Dinh, Neil M. Ferguson, Huizhi Gao, Verity Hill, Natsuko Imai, Michael A. Johansson, Sarah Kada, Oliver Morgan, Ana Pastore y Piontti, Jonathan A. Polonsky, Pragati Venkata Prasad, Talia M. Quandelacy, Andrew Rambaut, Jordan W. Tappero, Katelijn A. Vandemaele, Alessandro Vespignani, K. Lane Warmbrod, and Jessica Y. Wong
- Subjects
COVID-19 ,epidemiological parameters ,mathematical modeling ,World Health Organization ,coronavirus ,viruses ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
We report key epidemiologic parameter estimates for coronavirus disease identified in peer-reviewed publications, preprint articles, and online reports. Range estimates for incubation period were 1.8–6.9 days, serial interval 4.0–7.5 days, and doubling time 2.3–7.4 days. The effective reproductive number varied widely, with reductions attributable to interventions. Case burden and infection fatality ratios increased with patient age. Implementation of combined interventions could reduce cases and delay epidemic peak up to 1 month. These parameters for transmission, disease severity, and intervention effectiveness are critical for guiding policy decisions. Estimates will likely change as new information becomes available.
- Published
- 2020
- Full Text
- View/download PDF
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