Last data update: Apr 29, 2024. (Total: 46658 publications since 2009)
Records 1-30 (of 353 Records) |
Query Trace: Wong K[original query] |
---|
Examining state licensing requirements for select Master's-level behavioral health providers for children
Musburger P , Olson E , Etow A , Camilleri C , Wong H , Witten MH , Kaminski JW . Psychiatr Serv 2024 appips20230306 OBJECTIVE: The authors examined licensing requirements for select children's behavioral health care providers. METHODS: Statutes and regulations as of October 2021 were reviewed for licensed clinical social workers, licensed professional counselors, and licensed marriage and family therapists for all 50 U.S. states and the District of Columbia. RESULTS: All jurisdictions had laws regarding postgraduate training and license portability. No jurisdiction included language about specialized postgraduate training related to serving children and families or cultural competence. Other policies that related to the structure, composition, and authority of licensing boards varied across states and licensure types. CONCLUSIONS: In their efforts to address barriers to licensure, expand the workforce, and ensure that children have access to high-quality and culturally responsive care, states could consider their statutes and regulations. |
Influence of eat, sleep, and console on infants pharmacologically treated for opioid withdrawal: A post hoc subgroup analysis of the ESC-NOW randomized clinical trial
Devlin LA , Hu Z , Merhar SL , Ounpraseuth ST , Simon AE , Lee JY , Das A , Crawford MM , Greenberg RG , Smith PB , Higgins RD , Walsh MC , Rice W , Paul DA , Maxwell JR , Fung CM , Wright T , Ross J , McAllister JM , Crowley M , Shaikh SK , Christ L , Brown J , Riccio J , Wong Ramsey K , Braswell EF , Tucker L , McAlmon K , Dummula K , Weiner J , White JR , Newman S , Snowden JN , Young LW . JAMA Pediatr 2024 IMPORTANCE: The function-based eat, sleep, console (ESC) care approach substantially reduces the proportion of infants who receive pharmacologic treatment for neonatal opioid withdrawal syndrome (NOWS). This reduction has led to concerns for increased postnatal opioid exposure in infants who receive pharmacologic treatment. However, the effect of the ESC care approach on hospital outcomes for infants pharmacologically treated for NOWS is currently unknown. OBJECTIVE: To evaluate differences in opioid exposure and total length of hospital stay (LOS) for pharmacologically treated infants managed with the ESC care approach vs usual care with the Finnegan tool. DESIGN, SETTING, AND PARTICIPANTS: This post hoc subgroup analysis involved infants pharmacologically treated in ESC-NOW, a stepped-wedge cluster randomized clinical trial conducted at 26 US hospitals. Hospitals maintained pretrial practices for pharmacologic treatment, including opioid type, scheduled opioid dosing, and use of adjuvant medications. Infants were born at 36 weeks' gestation or later, had evidence of antenatal opioid exposure, and received opioid treatment for NOWS between September 2020 and March 2022. Data were analyzed from November 2022 to January 2024. EXPOSURE: Opioid treatment for NOWS and the ESC care approach. MAIN OUTCOMES AND MEASURES: For each outcome (total opioid exposure, peak opioid dose, time from birth to initiation of first opioid dose, length of opioid treatment, and LOS), we used generalized linear mixed models to adjust for the stepped-wedge design and maternal and infant characteristics. RESULTS: In the ESC-NOW trial, 463 of 1305 infants were pharmacologically treated (143/603 [23.7%] in the ESC care approach group and 320/702 [45.6%] in the usual care group). Mean total opioid exposure was lower in the ESC care approach group with an absolute difference of 4.1 morphine milligram equivalents per kilogram (MME/kg) (95% CI, 1.3-7.0) when compared with usual care (4.8 MME/kg vs 8.9 MME/kg, respectively; P = .001). Mean time from birth to initiation of pharmacologic treatment was 22.4 hours (95% CI, 7.1-37.7) longer with the ESC care approach vs usual care (75.4 vs 53.0 hours, respectively; P = .002). No significant difference in mean peak opioid dose was observed between groups (ESC care approach, 0.147 MME/kg, vs usual care, 0.126 MME/kg). The mean length of treatment was 6.3 days shorter (95% CI, 3.0-9.6) in the ESC care approach group vs usual care group (11.8 vs 18.1 days, respectively; P < .001), and mean LOS was 6.2 days shorter (95% CI, 3.0-9.4) with the ESC care approach than with usual care (16.7 vs 22.9 days, respectively; P < .001). CONCLUSION AND RELEVANCE: When compared with usual care, the ESC care approach was associated with less opioid exposure and shorter LOS for infants pharmacologically treated for NOWS. The ESC care approach was not associated with a higher peak opioid dose, although pharmacologic treatment was typically initiated later. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04057820. |
Integrating public health and health care - protecting health as a team sport
Wong CA , Houry D , Cohen MK . N Engl J Med 2024 |
Perceptions of Dengue risk and acceptability of a dengue vaccine in residents of Puerto Rico
Rosado-Santiago C , Pérez-Guerra CL , Vélez-Agosto NM , Colón-Burgos C , Marrero-Santos KM , Partridge SK , Lockwood AE , Young C , Waterman SH , Paz-Bailey G , Cardona-Gerena I , Rivera A , Adams LE , Wong JM . Hum Vaccin Immunother 2024 20 (1) 2323264 Dengvaxia is the first dengue vaccine recommended in the United States (U.S.). It is recommended for children aged 9-16 y with laboratory-confirmed previous dengue infection and living in areas where dengue is endemic. We conducted focus groups with parents and in-depth interviews with key informants (i.e. practicing pediatricians, physicians from immunization clinics, university researchers, and school officials) in Puerto Rico (P.R.) to examine acceptability, barriers, and motivators to vaccinate with Dengvaxia. We also carried out informal meetings and semi-structured interviews to evaluate key messages and educational materials with pediatricians and parents. Barriers to vaccination included lack of information, distrust toward new vaccines, vaccine side effects and risks, and high cost of/lack of insurance coverage for laboratory tests and vaccines. Motivators included clear information about the vaccine, a desire to prevent future dengue infections, the experience of a previous dengue infection or awareness of dengue fatality, vaccine and laboratory tests covered by health insurance, availability of rapid test results and vaccine appointments. School officials and parents agreed parents would pay a deductible of $5-20 for Dengvaxia. For vaccine information dissemination, parents preferred an educational campaign through traditional media and social media, and one-on-one counseling of parents by healthcare providers. Education about this vaccine to healthcare providers will help them answer parents' questions. Dengvaxia acceptability in P.R. will increase by addressing motivators and barriers to vaccination and by disseminating vaccine information in plain language through spokespersons from health institutions in P.R. |
Epidemiology and treatment outcomes of tuberculosis with chronic hepatitis B infection-California, 2016-2020
Bertumen JB , Pascopella L , Han E , Glenn-Finer R , Wong RJ , Chitnis A , Jaganath D , Jewell M , Gounder P , McElroy S , Stockman L , Barry P . Clin Infect Dis 2024 BACKGROUND: Improved epidemiologic and treatment data for active tuberculosis (TB) with chronic hepatitis B virus (cHBV) infection might inform and encourage screening and vaccination programs focused on persons at risk of having both conditions. METHODS: We matched the California Department of Public Health TB registry during 2016-2020 to the cHBV registry using probabilistic matching algorithms. We used chi-square analysis to compare the characteristics of persons with TB and cHBV with those with TB only. We compared TB treatment outcomes between these groups using modified Poisson regression models. We calculated the time between reporting of TB and cHBV diagnoses for those with both conditions. RESULTS: We identified 8,435 persons with TB, including 316 (3.7%) with cHBV.- Among persons with TB and cHBV, 256 (81.0%) were non-U.S.-born Asian vs 4,186 (51.6%) with TB only (P <0.0001). End-stage renal disease (26 [8.2%] vs 322 [4.0%]; P <0.001) and HIV (21 [6.7%] vs 247 [3.0%]; P value = 0.02) were more frequent among those with TB and cHBV compared with those with TB only. Among those with both conditions, 35 (11.1%) had TB diagnosed >60 days before cHBV (median 363 days) and 220 (69.6%) had TB diagnosed >60 days after cHBV (median 3,411 days). CONCLUSION: Persons with TB and cHBV were found more frequently in certain groups compared with TB only, and infrequently had their conditions diagnosed together. This highlights an opportunity to improve screening and treatment of TB and cHBV in those at high risk for coinfection. |
Social network strategy (SNS) for HIV testing: a new approach for identifying individuals with undiagnosed HIV infection in Tanzania
Rwabiyago OE , Katale A , Bingham T , Grund JM , Machangu O , Medley A , Nkomela ZM , Kayange A , King'ori GN , Juma JM , Ismail A , Kategile U , Akom E , Mlole NT , Schaad N , Maokola W , Nyagonde N , Magesa D , Kazitanga JC , Maruyama H , Temu F , Kimambo S , Sando D , Mbatia R , Chalamila ST , Ogwang BE , Njelekela MA , Kazaura K , Wong VJ , Gongo R , Njau PF , Mbunda A , Nondi J , Bateganya M , Greene J , Breda M , Mgomella G , Rwebembera A , Swaminathan M . AIDS Care 2024 1-10 Social network strategy (SNS) testing uses network connections to refer individuals at high risk to HIV testing services (HTS). In Tanzania, SNS testing is offered in communities and health facilities. In communities, SNS testing targets key and vulnerable populations (KVP), while in health facilities it complements index testing by reaching unelicited index contacts. Routine data were used to assess performance and trends over time in PEPFAR-supported sites between October 2021 and March 2023. Key indicators included SNS social contacts tested, and new HIV-positives individuals identified. Descriptive and statistical analysis were conducted. Univariable and multivariable analysis were applied, and variables with P-values <0.2 at univariable analysis were considered for multivariable analysis. Overall, 121,739 SNS contacts were tested, and 7731 (6.4%) previously undiagnosed individuals living with HIV were identified. Tested contacts and identified HIV-positives were mostly aged ≥15 years (>99.7%) and females (80.6% of tests, 79.4% of HIV-positives). Most SNS contacts were tested (78,363; 64.7%) and diagnosed (6376; 82.5%) in communities. SNS tests and HIV-positives grew 11.5 and 6.1-fold respectively, from October-December 2021 to January-March 2023, with majority of clients reached in communities vs. facilities (78,763 vs. 42,976). These results indicate that SNS testing is a promising HIV case-finding approach in Tanzania. |
Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal
Wong W , Schaffner SF , Thwing J , Seck MC , Gomis J , Diedhiou Y , Sy N , Ndiop M , Ba F , Diallo I , Sene D , Diallo MA , Ndiaye YD , Sy M , Sene A , Sow D , Dieye B , Tine A , Ribado J , Suresh J , Lee A , Battle KE , Proctor JL , Bever CA , MacInnis B , Ndiaye D , Hartl DL , Wirth DF , Volkman SK . Malar J 2024 23 (1) 68 BACKGROUND: Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programmes (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. METHODS: This study examined parasites from 3147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, a series of Poisson generalized linear mixed-effects models were constructed to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. RESULTS: Model-predicted incidence was compared with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (< 10/1000/annual [‰]). CONCLUSIONS: When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence > 10‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was < 10‰, many of the correlations between parasite genetics and incidence were reversed, which may reflect the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low. |
COVID-19 Vaccine Safety Technical (VaST) work group: Enhancing vaccine safety monitoring during the pandemic
Markowitz LE , Hopkins RH Jr , Broder KR , Lee GM , Edwards KM , Daley MF , Jackson LA , Nelson JC , Riley LE , McNally VV , Schechter R , Whitley-Williams PN , Cunningham F , Clark M , Ryan M , Farizo KM , Wong HL , Kelman J , Beresnev T , Marshall V , Shay DK , Gee J , Woo J , McNeil MM , Su JR , Shimabukuro TT , Wharton M , Keipp Talbot H . Vaccine 2024 During the COVID-19 pandemic, candidate COVID-19 vaccines were being developed for potential use in the United States on an unprecedented, accelerated schedule. It was anticipated that once available, under U.S. Food and Drug Administration (FDA) Emergency Use Authorization (EUA) or FDA approval, COVID-19 vaccines would be broadly used and potentially administered to millions of individuals in a short period of time. Intensive monitoring in the post-EUA/licensure period would be necessary for timely detection and assessment of potential safety concerns. To address this, the Centers for Disease Control and Prevention (CDC) convened an Advisory Committee on Immunization Practices (ACIP) work group focused solely on COVID-19 vaccine safety, consisting of independent vaccine safety experts and representatives from federal agencies - the ACIP COVID-19 Vaccine Safety Technical Work Group (VaST). This report provides an overview of the organization and activities of VaST, summarizes data reviewed as part of the comprehensive effort to monitor vaccine safety during the COVID-19 pandemic, and highlights selected actions taken by CDC, ACIP, and FDA in response to accumulating post-authorization safety data. VaST convened regular meetings over the course of 29 months, from November 2020 through April 2023; through March 2023 FDA issued EUAs for six COVID-19 vaccines from four different manufacturers and subsequently licensed two of these COVID-19 vaccines. The independent vaccine safety experts collaborated with federal agencies to ensure timely assessment of vaccine safety data during this time. VaST worked closely with the ACIP COVID-19 Vaccines Work Group; that work group used safety data and VaST's assessments for benefit-risk assessments and guidance for COVID-19 vaccination policy. Safety topics reviewed by VaST included those identified in safety monitoring systems and other topics of scientific or public interest. VaST provided guidance to CDC's COVID-19 vaccine safety monitoring efforts, provided a forum for review of data from several U.S. government vaccine safety systems, and assured that a diverse group of scientists and clinicians, external to the federal government, promptly reviewed vaccine safety data. In the event of a future pandemic or other biological public health emergency, the VaST model could be used to strengthen vaccine safety monitoring, enhance public confidence, and increase transparency through incorporation of independent, non-government safety experts into the monitoring process, and through strong collaboration among federal and other partners. |
Power law for estimating underdetection of foodborne disease outbreaks, United States
Ford L , Self JL , Wong KK , Hoekstra RM , Tauxe RV , Rose EB , Bruce BB . Emerg Infect Dis 2023 30 (2) 337-340 We fit a power law distribution to US foodborne disease outbreaks to assess underdetection and underreporting. We predicted that 788 fewer than expected small outbreaks were identified annually during 1998-2017 and 365 fewer during 2018-2019, after whole-genome sequencing was implemented. Power law can help assess effectiveness of public health interventions. |
Caregiver perspectives on barriers and facilitators to timely well-child visits for black infants
Dever R , Wong CA , Franklin MS , Howard J , Cholera R . Matern Child Health J 2024 OBJECTIVES: Missed infant well-child visits (WCV) result in lost opportunities for critical preventive care. Black infants consistently receive less WCV care than other racial groups. We sought to understand barriers and facilitators to timely infant WCV for Black families in the context of COVID-19. METHODS: We conducted 21 semi-structured interviews with caregivers of Medicaid-insured Black children aged 15- to 24-months who attended six or fewer of eight recommended well-child visits within the first 15 months of life. Interviews focused on WCV value, barriers, and facilitators. After developing our initial coding structure through rapid qualitative analysis, we inductively derived the final codebook and themes through line-by-line content analysis. RESULTS: Caregivers attended a mean of 3.53 of eight infant visits. Structural (e.g., transportation) and psychological (e.g., maternal depression) barriers delayed Black infant WCV. Families most frequently valued monitoring development and addressing concerns. Caregivers perceived visits as less urgent when infants seemed healthy or more recently avoided visits due to fears around COVID-19. Long waits and feeling rushed/dismissed were linked to WCV delays; positive provider relationships encouraged WCV attendance. Most caregivers reported reluctance to vaccinate. Vaccine hesitancy contributed to delayed infant WCV. CONCLUSIONS: Caregivers described several factors that impacted WCV attendance for Black infants. Persistent structural and psychological barriers are compounded by perceptions that caregiver time is not respected and by notable vaccine hesitancy. To address these barriers, well-care can meet Black families in their communities, better address caregiver wellbeing, more efficiently use caregiver and provider time, and cultivate partnerships with Black caregivers. |
Author Correction: Ultra-long-acting in-situ forming implants with cabotegravir protect female macaques against rectal SHIV infection
Young IC , Massud I , Cottrell ML , Shrivastava R , Maturavongsadit P , Prasher A , Wong-Sam A , Dinh C , Edwards T , Mrotz V , Mitchell J , Seixas JN , Pallerla A , Thorson A , Schauer A , Sykes C , De la Cruz G , Montgomery SA , Kashuba ADM , Heneine W , Dobard CW , Kovarova M , Garcia JV , Garcίa-Lerma JG , Benhabbour SR . Nat Commun 2024 15 (1) 1054 |
Strengthening the WHO Regional Office for Africa (WHO AFRO) COVID-19 vaccination information system
Shragai T , Bukhari A , Atagbaza AO , Oyaole DR , Shah R , Volkmann K , Kamau L , Sheillah N , Farham B , Wong MK , Lam E , Mboussou F , Impouma B . BMJ Glob Health 2024 9 (1) This manuscript describes the process and impact of strengthening the WHO Regional Office for Africa (WHO AFRO)'s COVID-19 vaccination information system. This system plays a critical role in tracking vaccination coverage, guiding resource allocation and supporting vaccination campaign roll-out for countries in the African region. Recognising existing data management issues, including complex reporting prone to human error, compromised data quality and underutilisation of collected data, WHO AFRO introduced significant system improvements during the COVID-19 pandemic. These improvements include shifting from an Excel-based to an online Azure-based data collection system, automating data processing and validation, and expansion of collected data. These changes have led to improvements in data quality and quantity including a decrease in data non-validity, missingness, and record duplication, and expansion of data collection forms to include a greater number of data fields, offering a more comprehensive understanding of vaccination efforts. Finally, the creation of accessible information products-including an interactive public dashboard, a weekly data pack and a public monthly bulletin-has improved data use and reach to relevant partners. These resources provide crucial insights into the region's vaccination progress at national and subnational levels, thereby enabling data-driven decision-making to improve programme performance. Overall, the strengthening of the WHO AFRO COVID-19 vaccination information system can serve as a model for similar efforts in other WHO regions and contexts. The impact of system strengthening on data quality demonstrated here underscores the vital role of robust data collection, capacity building and management systems in achieving high-quality data on vaccine distribution and coverage. Continued investment in information systems is essential for effective and equitable public health efforts. |
Detecting Mpox cases through wastewater surveillance - United States, August 2022-May 2023
Adams C , Kirby AE , Bias M , Riser A , Wong KK , Mercante JW , Reese H . MMWR Morb Mortal Wkly Rep 2024 73 (2) 37-43 In October 2022, CDC's National Wastewater Surveillance System began routine testing of U.S. wastewater for Monkeypox virus. Wastewater surveillance sensitivity, positive predictive value (PPV), and negative predictive value (NPV) for Monkeypox virus were evaluated by comparing wastewater detections (Monkeypox virus detected versus not detected) to numbers of persons with mpox in a county who were shedding virus. Case ascertainment was assumed to be complete, and persons with mpox were assumed to shed virus for 25 days after symptom onset. A total of 281 cases and 3,492 wastewater samples from 89 sites in 26 counties were included in the analysis. Wastewater surveillance in a single week, from samples representing thousands to millions of persons, had a sensitivity of 32% for detecting one or more persons shedding Monkeypox virus, 49% for detecting five or more persons shedding virus, and 77% for detecting 15 or more persons shedding virus. Weekly PPV and NPV for detecting persons shedding Monkeypox virus in a county were 62% and 80%, respectively. An absence of detections in counties with wastewater surveillance signified a high probability that a large number of cases were not present. Results can help to guide the public health response to Monkeypox virus wastewater detections. A single, isolated detection likely warrants a limited public health response. An absence of detections, in combination with no reported cases, can give public health officials greater confidence that no cases are present. Wastewater surveillance can serve as a useful complement to case surveillance for guiding the public health response to an mpox outbreak. |
Comparison of factors associated with seasonal influenza and COVID-19 booster vaccination coverage among healthcare personnel working at acute care hospitals during 2021-2022 influenza season, National Healthcare Safety Network, United States
Meng L , Bell J , Soe M , Edwards J , Lymon H , Barbre K , Reses H , Patel A , Wong E , Dudeck M , Huynh CV , Rowe T , Dubendris H , Benin A . Prev Med 2024 179 107852 The simultaneous circulation of seasonal influenza virus and SARS-CoV-2 variants will likely pose unique challenges to public health during the future influenza seasons. Persons who are undergoing treatment in healthcare facilities may be particularly at risk. It is important for healthcare personnel to protect themselves and patients by receiving vaccines. The purpose of this study is to assess coverage of the seasonal influenza vaccine and COVID-19 monovalent booster among healthcare personnel working at acute care hospitals in the United States during the 2021-22 influenza season and to examine the demographic and facility characteristics associated with coverage. A total of 3260 acute care hospitals with over 7 million healthcare personnel reported vaccination data to National Healthcare Safety Network (NHSN) during the 2021-22 influenza season. Two separate negative binomial mixed models were developed to explore the factors associated with seasonal influenza coverage and COVID-19 monovalent booster coverage. At the end of the 2021-2022 influenza season, the overall pooled mean seasonal influenza coverage was 80.3%, and the pooled mean COVID-19 booster coverage was 39.5%. Several demographic and facility-level factors, such as employee type, facility ownership, and geographic region, were significantly associated with vaccination against influenza and COVID-19 among healthcare personnel working in acute care hospitals. Our findings highlight the need to increase the uptake of vaccination among healthcare personnel, particularly non-employees, those working in for-profit and non-medical school-affiliated facilities, and those residing in the South. |
Pharmacokinetic study of islatravir and etonogestrel implants in macaques
Daly MB , Wong-Sam A , Li L , Krovi A , Gatto GJ , Norton C , Luecke EH , Mrotz V , Forero C , Cottrell ML , Schauer AP , Gary J , Nascimento-Seixas J , Mitchell J , van der Straten A , Heneine W , Garcίa-Lerma JG , Dobard CW , Johnson LM . Pharmaceutics 2023 15 (12) The prevention of HIV and unintended pregnancies is a public health priority. Multi-purpose prevention technologies capable of long-acting HIV and pregnancy prevention are desirable for women. Here, we utilized a preclinical macaque model to evaluate the pharmacokinetics of biodegradable ε-polycaprolactone implants delivering the antiretroviral islatravir (ISL) and the contraceptive etonogestrel (ENG). Three implants were tested: ISL-62 mg, ISL-98 mg, and ENG-33 mg. Animals received one or two ISL-eluting implants, with doses of 42, 66, or 108 µg of ISL/day with or without an additional ENG-33 mg implant (31 µg/day). Drug release increased linearly with dose with median [range] plasma ISL levels of 1.3 [1.0-2.5], 1.9 [1.2-6.3] and 2.8 [2.3-11.6], respectively. The ISL-62 and 98 mg implants demonstrated stable drug release over three months with ISL-triphosphate (ISL-TP) concentr54ations in PBMCs above levels predicted to be efficacious for PrEP. Similarly, ENG implants demonstrated sustained drug release with median [range] plasma ENG levels of 495 [229-1110] pg/mL, which suppressed progesterone within two weeks and showed no evidence of altering ISL pharmacokinetics. Two of the six ISL-98 mg implants broke during the study and induced implant-site reactions, whereas no reactions were observed with intact implants. We show that ISL and ENG biodegradable implants are safe and yield sufficient drug levels to achieve prevention targets. The evaluation of optimized implants with increased mechanical robustness is underway for improved durability and vaginal efficacy in a SHIV challenge model. |
The impact of COVID-19 on healthcare coverage and access in racial and ethnic minority populations in the United States
Freelander L , Rickless DS , Anderson C , Curriero F , Rockhill S , Mirsajedin A , Colón CJ , Lusane J , Vigo-Valentín A , Wong D . Geospat Health 2023 18 (2) This study described spatiotemporal changes in health insurance coverage, healthcare access, and reasons for non-insurance among racial/ethnic minority populations in the United States during the COVID-19 pandemic using four national survey datasets. Getis-Ord Gi* statistic and scan statistics were used to analyze geospatial clusters of health insurance coverage by race/ethnicity. Logistic regression was used to estimate odds of reporting inability to access healthcare across two pandemic time periods by race/ethnicity. Racial/ethnic differences in insurance were observed from 2010 through 2019, with the lowest rates being among Hispanic/Latino, African American, American Indian/Alaska Native, and Native Hawaiian/Pacific Islander populations. Pre-pandemic insurance coverage rates were geographically clustered. The percentage of adults citing change in employment status as the reason for non-insurance increased by about 7% after the start of the pandemic, with a small decrease observed among African American adults. Almost half of adults reported reduced healthcare access in June 2020, with 38.7% attributing reduced access to the pandemic; however, by May 2021, the percent of respondents reporting reduced access for any reason and due to the pandemic fell to 26.9% and 12.7%, respectively. In general, racial/ethnic disparities in health insurance coverage and healthcare access worsened during the pandemic. Although coverage and access improved over time, pre-COVID disparities persisted with African American and Hispanic/Latino populations being the most affected by insurance loss and reduced healthcare access. Cost, unemployment, and eligibility drove non-insurance before and during the pandemic. |
Evaluating the performance of Plasmodium falciparum genetics for inferring National Malaria Control Program reported incidence in Senegal
Wong W , Schaffner SF , Thwing J , Seck MC , Gomis J , Diedhiou Y , Sy N , Ndiop M , Ba F , Diallo I , Sene D , Diallo MA , Ndiaye YD , Sy M , Sene A , Sow D , Dieye B , Tine A , Ribado J , Suresh J , Lee A , Battle KE , Proctor JL , Bever CA , MacInnis B , Ndiaye D , Hartl DL , Wirth DF , Volkman SK . Res Sq 2023 Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programs (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. Here, we examined parasites from 3,147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, we constructed a series of Poisson generalized linear mixed-effects models to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. We compared the model-predicted incidence with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (<10/1000/annual [‰]). When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence >10 ‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was <10 ‰, we found that many of the correlations between parasite genetics and incidence were reversed, which we hypothesize reflects the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low. |
Lessons learned from applying a monitoring and evaluation framework to economic, social, and other health impacts of the COVID-19 pandemic
Laurent AA , Vo L , Wong EY . Public Health Rep 2023 139 (1) 333549231208489 Individual and community-level COVID-19 mitigation policies can have effects beyond direct COVID-19 health outcomes, including social, behavioral, and economic outcomes. These social, behavioral, and economic outcomes can extend beyond the pandemic period and have disparate effects on populations. Public Health-Seattle & King County (PHSKC) built on the Centers for Disease Control and Prevention's community mitigation strategy framework to create a local project tracking near-real-time data to understand factors affected by mitigation approaches, inform decision-making, and monitor and evaluate community-level disparities during the pandemic. This case study describes the framework and lessons learned from PHSKC's collation, use, and dissemination of local data from 20 data sources to guide community and public health decision-making. Social, behavioral, economic, and health indicators were regularly updated and disseminated through interactive dashboards and products that examined data in the context of applicable policies. Data disaggregated by demographic characteristics and geography highlighted inequities, but not all datasets contained the same details; local surveys or qualitative data were used to fill gaps. Project outcomes included informing city and county emergency response planning related to implementation of financial and food assistance programs. Key lessons learned included the need to (1) build on existing processes and use automated processes and (2) partner with other sectors to use nontraditional public health data for active dissemination and data disaggregation and for real-time data contextualized by policy changes. This project provided programs and communities with timely, reliable data to understand where to invest recovery funding. A similar framework could position other health departments to examine social and economic effects during future public health emergencies. |
Influenza and up-to-date COVID-19 vaccination coverage among health care personnel - National Healthcare Safety Network, United States, 2022-23 Influenza Season
Bell J , Meng L , Barbre K , Haanschoten E , Reses HE , Soe M , Edwards J , Massey J , Tugu Yagama Reddy GR , Woods A , Stuckey MJ , Kuhar DT , Bolden K , Dubendris H , Wong E , Rowe T , Lindley MC , Kalayil EJ , Benin A . MMWR Morb Mortal Wkly Rep 2023 72 (45) 1237-1243 The Advisory Committee on Immunization Practices recommends that health care personnel (HCP) receive an annual influenza vaccine and that everyone aged ≥6 months stay up to date with recommended COVID-19 vaccination. Health care facilities report vaccination of HCP against influenza and COVID-19 to CDC's National Healthcare Safety Network (NHSN). During January-June 2023, NHSN defined up-to-date COVID-19 vaccination as receipt of a bivalent COVID-19 mRNA vaccine dose or completion of a primary series within the preceding 2 months. This analysis describes influenza and up-to-date COVID-19 vaccination coverage among HCP working in acute care hospitals and nursing homes during the 2022-23 influenza season (October 1, 2022-March 31, 2023). Influenza vaccination coverage was 81.0% among HCP at acute care hospitals and 47.1% among those working at nursing homes. Up-to-date COVID-19 vaccination coverage was 17.2% among HCP working at acute care hospitals and 22.8% among those working at nursing homes. There is a need to promote evidence-based strategies to improve vaccination coverage among HCP. Tailored strategies might also be useful to reach all HCP with recommended vaccines and protect them and their patients from vaccine-preventable respiratory diseases. |
Declines in influenza vaccination coverage among health care personnel in acute care hospitals during the COVID-19 pandemic - United States, 2017-2023
Lymon H , Meng L , Reses HE , Barbre K , Dubendris H , Shafi S , Wiegand R , Reddy Grty , Woods A , Kuhar DT , Stuckey MJ , Lindley MC , Haas L , Qureshi I , Wong E , Benin A , Bell JM . MMWR Morb Mortal Wkly Rep 2023 72 (45) 1244-1247 Health care personnel (HCP) are recommended to receive annual vaccination against influenza to reduce influenza-related morbidity and mortality. Every year, acute care hospitals report receipt of influenza vaccination among HCP to CDC's National Healthcare Safety Network (NHSN). This analysis used NHSN data to describe changes in influenza vaccination coverage among HCP in acute care hospitals before and during the COVID-19 pandemic. Influenza vaccination among HCP increased during the prepandemic period from 88.6% during 2017-18 to 90.7% during 2019-20. During the COVID-19 pandemic, the percentage of HCP vaccinated against influenza decreased to 85.9% in 2020-21 and 81.1% in 2022-23. Additional efforts are needed to implement evidence-based strategies to increase vaccination coverage among HCP and to identify factors associated with recent declines in influenza vaccination coverage. |
Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal
Schaffner SF , Badiane A , Khorgade A , Ndiop M , Gomis J , Wong W , Ndiaye YD , Diedhiou Y , Thwing J , Seck MC , Early A , Sy M , Deme A , Diallo MA , Sy N , Sene A , Ndiaye T , Sow D , Dieye B , Ndiaye IM , Gaye A , Ndiaye A , Battle KE , Proctor JL , Bever C , Fall FB , Diallo I , Gaye S , Sene D , Hartl DL , Wirth DF , MacInnis B , Ndiaye D , Volkman SK . Nat Commun 2023 14 (1) 7268 We here analyze data from the first year of an ongoing nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal. The analysis is based on 1097 samples collected at health facilities during passive malaria case detection in 2019; it provides a baseline for analyzing parasite genetic metrics as they vary over time and geographic space. The study's goal was to identify genetic metrics that were informative about transmission intensity and other aspects of transmission dynamics, focusing on measures of genetic relatedness between parasites. We found the best genetic proxy for local malaria incidence to be the proportion of polygenomic infections (those with multiple genetically distinct parasites), although this relationship broke down at low incidence. The proportion of related parasites was less correlated with incidence while local genetic diversity was uninformative. The type of relatedness could discriminate local transmission patterns: two nearby areas had similarly high fractions of relatives, but one was dominated by clones and the other by outcrossed relatives. Throughout Senegal, 58% of related parasites belonged to a single network of relatives, within which parasites were enriched for shared haplotypes at known and suspected drug resistance loci and at one novel locus, reflective of ongoing selection pressure. |
COVID-19 epidemiology during Delta variant dominance period in 45 high-income countries, 2020-2021
Atherstone CJ , Guagliardo SAJ , Hawksworth A , O'Laughlin K , Wong K , Sloan ML , Henao O , Rao CY , McElroy PD , Bennett SD . Emerg Infect Dis 2023 29 (9) 1757-1764 The SARS-CoV-2 Delta variant, first identified in October 2020, quickly became the dominant variant worldwide. We used publicly available data to explore the relationship between illness and death (peak case rates, death rates, case-fatality rates) and selected predictors (percentage vaccinated, percentage of the population >65 years, population density, testing volume, index of mitigation policies) in 45 high-income countries during the Delta wave using rank-order correlation and ordinal regression. During the Delta-dominant period, most countries reported higher peak case rates (57%) and lower peak case-fatality rates (98%). Higher vaccination coverage was protective against peak case rates (odds ratio 0.95, 95% CI 0.91-0.99) and against peak death rates (odds ratio 0.96, 95% CI 0.91-0.99). Vaccination coverage was vital to preventing infection and death from COVID-19 during the Delta wave. As new variants emerge, public health authorities should encourage the uptake of COVID-19 vaccination and boosters. |
Adapting shift work schedules for sleep quality, sleep duration, and sleepiness in shift workers
Hulsegge G , Coenen P , Gascon GM , Pahwa M , Greiner B , Bohane C , Wong IS , Liira J , Riera R , Pachito DV . Cochrane Database Syst Rev 2023 9 (9) Cd010639 BACKGROUND: Shift work is associated with insufficient sleep, which can compromise worker alertness with ultimate effects on occupational health and safety. Adapting shift work schedules may reduce adverse occupational outcomes. OBJECTIVES: To assess the effects of shift schedule adaptation on sleep quality, sleep duration, and sleepiness among shift workers. SEARCH METHODS: We searched CENTRAL, PubMed, Embase, and eight other databases on 13 December 2020, and again on 20 April 2022, applying no language restrictions. SELECTION CRITERIA: We included randomised controlled trials (RCTs) and non-RCTs, including controlled before-after (CBA) trials, interrupted time series, and cross-over trials. Eligible trials evaluated any of the following shift schedule components. • Permanency of shifts • Regularity of shift changes • Direction of shift rotation • Speed of rotation • Shift duration • Timing of start of shifts • Distribution of shift schedule • Time off between shifts • Split shifts • Protected sleep • Worker participation We included studies that assessed sleep quality off-shift, sleep duration off-shift, or sleepiness during shifts. DATA COLLECTION AND ANALYSIS: Two review authors independently screened the titles and abstracts of the records recovered by the search, read through the full-text articles of potentially eligible studies, and extracted data. We assessed the risk of bias of included studies using the Cochrane risk of bias tool, with specific additional domains for non-randomised and cluster-randomised studies. For all stages, we resolved any disagreements by consulting a third review author. We presented the results by study design and combined clinically homogeneous studies in meta-analyses using random-effects models. We assessed the certainty of the evidence with GRADE. MAIN RESULTS: We included 11 studies with a total of 2125 participants. One study was conducted in a laboratory setting and was not considered for drawing conclusions on intervention effects. The included studies investigated different and often multiple changes to shift schedule, and were heterogeneous with respect to outcome measurement. Forward versus backward rotation Three CBA trials (561 participants) investigated the effects of forward rotation versus backward rotation. Only one CBA trial provided sufficient data for the quantitative analysis; it provided very low-certainty evidence that forward rotation compared with backward rotation did not affect sleep quality measured with the Basic Nordic Sleep Questionnaire (BNSQ; mean difference (MD) -0.20 points, 95% confidence interval (CI) -2.28 to 1.89; 62 participants) or sleep duration off-shift (MD -0.21 hours, 95% CI -3.29 to 2.88; 62 participants). However, there was also very low-certainty evidence that forward rotation reduced sleepiness during shifts measured with the BNSQ (MD -1.24 points, 95% CI -2.24 to -0.24; 62 participants). Faster versus slower rotation Two CBA trials and one non-randomised cross-over trial (341 participants) evaluated faster versus slower shift rotation. We were able to meta-analyse data from two studies. There was low-certainty evidence of no difference in sleep quality off-shift (standardised mean difference (SMD) -0.01, 95% CI -0.26 to 0.23) and very low-certainty evidence that faster shift rotation reduced sleep duration off-shift (SMD -0.26, 95% CI -0.51 to -0.01; 2 studies, 282 participants). The SMD for sleep duration translated to an MD of 0.38 hours' less sleep per day (95% CI -0.74 to -0.01). One study provided very low-certainty evidence that faster rotations decreased sleepiness during shifts measured with the BNSQ (MD -1.24 points, 95% CI -2.24 to -0.24; 62 participants). Limited shift duration (16 hours) versus unlimited shift duration Two RCTs (760 participants) evaluated 80-hour workweeks with maximum daily shift duration of 16 hours versus workweeks without any daily shift duration limits. There was low-certainty evidence that the 16-hour limit increased sleep duration off-shift (SMD 0.50, 95% CI 0.21 to 0.78; which translated to an MD of 0.73 hours' more sleep per day, 95% CI 0.30 to 1.13; 2 RCTs, 760 participants) and moderate-certainty evidence that the 16-hour limit reduced sleepiness during shifts, measured with the Karolinska Sleepiness Scale (SMD -0.29, 95% CI -0.44 to -0.14; which translated to an MD of 0.37 fewer points, 95% CI -0.55 to -0.17; 2 RCTs, 716 participants). Shorter versus longer shifts One RCT, one CBA trial, and one non-randomised cross-over trial (692 participants) evaluated shorter shift duration (eight to 10 hours) versus longer shift duration (two to three hours longer). There was very low-certainty evidence of no difference in sleep quality (SMD -0.23, 95% CI -0.61 to 0.15; which translated to an MD of 0.13 points lower on a scale of 1 to 5; 2 studies, 111 participants) or sleep duration off-shift (SMD 0.18, 95% CI -0.17 to 0.54; which translated to an MD of 0.26 hours' less sleep per day; 2 studies, 121 participants). The RCT and the non-randomised cross-over study found that shorter shifts reduced sleepiness during shifts, while the CBA study found no effect on sleepiness. More compressed versus more spread out shift schedules One RCT and one CBA trial (346 participants) evaluated more compressed versus more spread out shift schedules. The CBA trial provided very low-certainty evidence of no difference between the groups in sleep quality off-shift (MD 0.31 points, 95% CI -0.53 to 1.15) and sleep duration off-shift (MD 0.52 hours, 95% CI -0.52 to 1.56). AUTHORS' CONCLUSIONS: Forward and faster rotation may reduce sleepiness during shifts, and may make no difference to sleep quality, but the evidence is very uncertain. Very low-certainty evidence indicated that sleep duration off-shift decreases with faster rotation. Low-certainty evidence indicated that on-duty workweeks with shift duration limited to 16 hours increases sleep duration, with moderate-certainty evidence for minimal reductions in sleepiness. Changes in shift duration and compression of workweeks had no effect on sleep or sleepiness, but the evidence was of very low-certainty. No evidence is available for other shift schedule changes. There is a need for more high-quality studies (preferably RCTs) for all shift schedule interventions to draw conclusions on the effects of shift schedule adaptations on sleep and sleepiness in shift workers. |
SARS-CoV-2 infection and death rates among maintenance dialysis patients during Delta and early Omicron waves - United States, June 30, 2021-September 27, 2022
Navarrete J , Barone G , Qureshi I , Woods A , Barbre K , Meng L , Novosad S , Li Q , Soe MM , Edwards J , Wong E , Reses HE , Guthrie S , Keenan J , Lamping L , Park M , Dumbuya S , Benin AL , Bell J . MMWR Morb Mortal Wkly Rep 2023 72 (32) 871-876 Persons receiving maintenance dialysis are at increased risk for SARS-CoV-2 infection and its severe outcomes, including death. However, rates of SARS-CoV-2 infection and COVID-19-related deaths in this population are not well described. Since November 2020, CDC's National Healthcare Safety Network (NHSN) has collected weekly data monitoring incidence of SARS-CoV-2 infections (defined as a positive SARS-CoV-2 test result) and COVID-19-related deaths (defined as the death of a patient who had not fully recovered from a SARS-CoV-2 infection) among maintenance dialysis patients. This analysis used NHSN dialysis facility COVID-19 data reported during June 30, 2021-September 27, 2022, to describe rates of SARS-CoV-2 infection and COVID-19-related death among maintenance dialysis patients. The overall infection rate was 30.47 per 10,000 patient-weeks (39.64 among unvaccinated patients and 27.24 among patients who had completed a primary COVID-19 vaccination series). The overall death rate was 1.74 per 10,000 patient-weeks. Implementing recommended infection control measures in dialysis facilities and ensuring patients and staff members are up to date with recommended COVID-19 vaccination is critical to limiting COVID-19-associated morbidity and mortality. |
Vaccine safety surveillance in Kenya using GAIA standards: A feasibility assessment of existing national and subnational research and program systems
Izulla P , Wagai JN , Akelo V , Ombeva A , Okeri E , Onyango D , Omore R , Fuller S , Khagayi S , Were J , Anderson SA , Wong HL , Tippett Barr BA . Vaccine 2023 41 (39) 5722-5729 BACKGROUND: Active surveillance systems for monitoring vaccine safety among pregnant women address some of the limitations of a current passive surveillance approach utilized in low- and middle-income countries (LMIC). However, few active surveillance systems in LMIC exist. Our study assessed the feasibility of utilizing three existing data collection systems in Kenya for active surveillance of maternal immunization and to assess the applicability of Global Alignment of Immunization Safety Assessment in pregnancy (GAIA) case definitions that were initially developed for clinical trials within these systems. METHODS: We assessed applicability of GAIA case definition for maternal Tetanus Toxoid exposure, stillbirth, low birth weight, small for gestational age, Neonatal Invasive Blood Stream Infection (NIBSI), prematurity and neonatal death in two routine web-based health information systems (Kenya EMR and DHIS-2), and a web-based population-based pregnancy research platform (ANCOV(1)) in Kenya. RESULTS: All three HIS were capable of reporting selected outcomes to varying degrees of GAIA certainty. The ANCOV platform was the most robust in collecting and collating clinical data for effective maternal pharmacovigilance. The utilization of facility- and district-aggregated data limits the usefulness of DHIS-2 in pharmacovigilance as currently operationalized. While the Kenya EMR contained individual level data and meets the key considerations for effective pharmacovigilance, it was used primarily for HIV care and treatment records in a small proportion of health facilities and would require additional resources to expand to all antenatal care facilities and to link maternal and infant records. DISCUSSION: Population-based research studies may offer a responsive short-term option for implementing maternal vaccine pharmacovigilance in LMICs. However, the foundation exists for long-term capacity building within the national health electronic data systems to provide this critical service as well as ensure participation of the country in international studies on maternal vaccine safety. |
Arboviral vaccines for use in pregnant travelers
Hills SL , Wong JM , Staples JE . Travel Med Infect Dis 2023 55 102624 Pregnant women traveling abroad can be exposed to a variety of arboviruses, primarily spread by mosquitoes or ticks. Some arboviral infections can be of particular concern for pregnant women or their fetuses. Vaccination is one preventive measure that can reduce the risk for infection. Several arboviral vaccines have been licensed for many years and can be used to prevent infection in travelers, namely Japanese encephalitis, yellow fever, and tick-borne encephalitis vaccines. Recommendations on use of these vaccines in pregnancy vary. Other arboviral vaccines have been licensed but are not indicated for use in pregnant travelers (e.g., dengue vaccines) or are in development (e.g., chikungunya, Zika vaccines). This review describes arboviral vaccines for travelers, focusing on women who are pregnant and those planning travel during pregnancy. |
Travel-associated Dengue cases - United States, 2010-2021
Wong JM , Rivera A , Volkman HR , Torres-Velasquez B , Rodriguez DM , Paz-Bailey G , Adams LE . MMWR Morb Mortal Wkly Rep 2023 72 (30) 821-826 Dengue, the leading cause of arboviral disease worldwide, can be fatal without appropriate treatment. Among 7,528 confirmed or probable travel-associated U.S. dengue cases reported during 2010-2021, one in five (1,474, 20%) was reported in 2019. This is 168% higher than the annual average number of cases reported during 2010-2018 and 2020-2021 (approximately 550 per year) and 61% higher than the 913 cases reported in 2016, the second highest year on record. The number of cases as a fraction of air traffic volume to international destinations outside North America or Europe was also highest in 2019, with 41.9 cases per million trips, compared with 21.0 per million in other years during 2010-2021. This report compares the number and characteristics of travel-associated dengue cases reported to national surveillance in the United States in 2019 with cases reported during 2010-2018 and 2020-2021. Areas with conditions suitable for dengue transmission as well as the population at risk for dengue are expected to increase, placing U.S. travelers at higher risk for infection. Health care providers should be aware that dengue is a common cause of fever in the returning traveler and be familiar with its signs and symptoms, testing, and management. Dengue vaccines are not currently recommended for U.S. travelers; therefore, persons should review areas of dengue risk and follow guidance for preventing mosquito bites. |
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US (preprint)
Cramer EY , Ray EL , Lopez VK , Bracher J , Brennen A , Castro Rivadeneira AJ , Gerding A , Gneiting T , House KH , Huang Y , Jayawardena D , Kanji AH , Khandelwal A , Le K , Mühlemann A , Niemi J , Shah A , Stark A , Wang Y , Wattanachit N , Zorn MW , Gu Y , Jain S , Bannur N , Deva A , Kulkarni M , Merugu S , Raval A , Shingi S , Tiwari A , White J , Abernethy NF , Woody S , Dahan M , Fox S , Gaither K , Lachmann M , Meyers LA , Scott JG , Tec M , Srivastava A , George GE , Cegan JC , Dettwiller ID , England WP , Farthing MW , Hunter RH , Lafferty B , Linkov I , Mayo ML , Parno MD , Rowland MA , Trump BD , Zhang-James Y , Chen S , Faraone SV , Hess J , Morley CP , Salekin A , Wang D , Corsetti SM , Baer TM , Eisenberg MC , Falb K , Huang Y , Martin ET , McCauley E , Myers RL , Schwarz T , Sheldon D , Gibson GC , Yu R , Gao L , Ma Y , Wu D , Yan X , Jin X , Wang YX , Chen Y , Guo L , Zhao Y , Gu Q , Chen J , Wang L , Xu P , Zhang W , Zou D , Biegel H , Lega J , McConnell S , Nagraj VP , Guertin SL , Hulme-Lowe C , Turner SD , Shi Y , Ban X , Walraven R , Hong QJ , Kong S , van de Walle A , Turtle JA , Ben-Nun M , Riley S , Riley P , Koyluoglu U , DesRoches D , Forli P , Hamory B , Kyriakides C , Leis H , Milliken J , Moloney M , Morgan J , Nirgudkar N , Ozcan G , Piwonka N , Ravi M , Schrader C , Shakhnovich E , Siegel D , Spatz R , Stiefeling C , Wilkinson B , Wong A , Cavany S , España G , Moore S , Oidtman R , Perkins A , Kraus D , Kraus A , Gao Z , Bian J , Cao W , Lavista Ferres J , Li C , Liu TY , Xie X , Zhang S , Zheng S , Vespignani A , Chinazzi M , Davis JT , Mu K , Pastore YPiontti A , Xiong X , Zheng A , Baek J , Farias V , Georgescu A , Levi R , Sinha D , Wilde J , Perakis G , Bennouna MA , Nze-Ndong D , Singhvi D , Spantidakis I , Thayaparan L , Tsiourvas A , Sarker A , Jadbabaie A , Shah D , Della Penna N , Celi LA , Sundar S , Wolfinger R , Osthus D , Castro L , Fairchild G , Michaud I , Karlen D , Kinsey M , Mullany LC , Rainwater-Lovett K , Shin L , Tallaksen K , Wilson S , Lee EC , Dent J , Grantz KH , Hill AL , Kaminsky J , Kaminsky K , Keegan LT , Lauer SA , Lemaitre JC , Lessler J , Meredith HR , Perez-Saez J , Shah S , Smith CP , Truelove SA , Wills J , Marshall M , Gardner L , Nixon K , Burant JC , Wang L , Gao L , Gu Z , Kim M , Li X , Wang G , Wang Y , Yu S , Reiner RC , Barber R , Gakidou E , Hay SI , Lim S , Murray C , Pigott D , Gurung HL , Baccam P , Stage SA , Suchoski BT , Prakash BA , Adhikari B , Cui J , Rodríguez A , Tabassum A , Xie J , Keskinocak P , Asplund J , Baxter A , Oruc BE , Serban N , Arik SO , Dusenberry M , Epshteyn A , Kanal E , Le LT , Li CL , Pfister T , Sava D , Sinha R , Tsai T , Yoder N , Yoon J , Zhang L , Abbott S , Bosse NI , Funk S , Hellewell J , Meakin SR , Sherratt K , Zhou M , Kalantari R , Yamana TK , Pei S , Shaman J , Li ML , Bertsimas D , Skali Lami O , Soni S , Tazi Bouardi H , Ayer T , Adee M , Chhatwal J , Dalgic OO , Ladd MA , Linas BP , Mueller P , Xiao J , Wang Y , Wang Q , Xie S , Zeng D , Green A , Bien J , Brooks L , Hu AJ , Jahja M , McDonald D , Narasimhan B , Politsch C , Rajanala S , Rumack A , Simon N , Tibshirani RJ , Tibshirani R , Ventura V , Wasserman L , O'Dea EB , Drake JM , Pagano R , Tran QT , Ho LST , Huynh H , Walker JW , Slayton RB , Johansson MA , Biggerstaff M , Reich NG . medRxiv 2021 2021.02.03.21250974 Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. In 2020, the COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized hundreds of thousands of specific predictions from more than 50 different academic, industry, and independent research groups. This manuscript systematically evaluates 23 models that regularly submitted forecasts of reported weekly incident COVID-19 mortality counts in the US at the state and national level. One of these models was a multi-model ensemble that combined all available forecasts each week. The performance of individual models showed high variability across time, geospatial units, and forecast horizons. Half of the models evaluated showed better accuracy than a naïve baseline model. In combining the forecasts from all teams, the ensemble showed the best overall probabilistic accuracy of any model. Forecast accuracy degraded as models made predictions farther into the future, with probabilistic accuracy at a 20-week horizon more than 5 times worse than when predicting at a 1-week horizon. This project underscores the role that collaboration and active coordination between governmental public health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks.Competing Interest StatementAV, MC, and APP report grants from Metabiota Inc outside the submitted work.Funding StatementFor teams that reported receiving funding for their work, we report the sources and disclosures below. CMU-TimeSeries: CDC Center of Excellence, gifts from Google and Facebook. CU-select: NSF DMS-2027369 and a gift from the Morris-Singer Foundation. COVIDhub: This work has been supported by the US Centers for Disease Control and Prevention (1U01IP001122) and the National Institutes of General Medical Sciences (R35GM119582). The content is solely the responsibility of the authors and does not necessarily represent the official views of CDC, NIGMS or the National Institutes of Health. Johannes Bracher was supported by the Helmholtz Foundation via the SIMCARD Information& Data Science Pilot Project. Tilmann Gneiting gratefully acknowledges support by the Klaus Tschira Foundation. DDS-NBDS: NSF III-1812699. EPIFORECASTS-ENSEMBLE1: Wellcome Trust (210758/Z/18/Z) GT_CHHS-COVID19: William W. George Endowment, Virginia C. and Joseph C. Mello Endowments, NSF DGE-1650044, NSF MRI 1828187, research cyberinfrastructure resources and services provided by the Partnership for an Advanced Computing Environment (PACE) at Georgia Tech, and the following benefactors at Georgia Tech: Andrea Laliberte, Joseph C. Mello, Richard Rick E. & Charlene Zalesky, and Claudia & Paul Raines GT-DeepCOVID: CDC MInD-Healthcare U01CK000531-Supplement. NSF (Expeditions CCF-1918770, CAREER IIS-2028586, RAPID IIS-2027862, Medium IIS-1955883, NRT DGE-1545362), CDC MInD program, ORNL and funds/computing resources from Georgia Tech and GTRI. IHME: This work was supported by the Bill & Melinda Gates Foundation, as well as funding from the state of Washington and the National Science Foundation (award no. FAIN: 2031096). IowaStateLW-STEM: Iowa State University Plant Sciences Institute Scholars Program, NSF DMS-1916204, NSF CCF-1934884, Laurence H. Baker Center for Bioinformatics and Biological Statistics. JHU_IDD-CovidSP: State of California, US Dept of Health and Human Services, US Dept of Homeland Security, US Office of Foreign Disaster Assistance, Johns Hopkins Health System, Office of the Dean at Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University Modeling and Policy Hub, Centers fo Disease Control and Prevention (5U01CK000538-03), University of Utah Immunology, Inflammation, & Infectious Disease Initiative (26798 Seed Grant). LANL-GrowthRate: LANL LDRD 20200700ER. MOBS-GLEAM_COVID: COVID Supplement CDC-HHS-6U01IP001137-01. NotreDame-mobility and NotreDame-FRED: NSF RAPID DEB 2027718 UA-EpiCovDA: NSF RAPID Grant # 2028401. UCSB-ACTS: NSF RAPID IIS 2029626. UCSD-NEU: Google Faculty Award, DARPA W31P4Q-21-C-0014, COVID Supplement CDC-HHS-6U01IP001137-01. UMass-MechBayes: NIGMS R35GM119582, NSF 1749854. UMich-RidgeTfReg: The University of Michigan Physics Department and the University of Michigan Office of Research.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:UMass-Amherst IRBAll 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.YesAll data and code referred to in the manuscript are publicly available. https://github.com/reichlab/covid19-forecast-hub/ https://github.com/reichlab/covidEnsembles https://zoltardata.com/project/44 |
Characteristics of children and antigen test performance at a SARS-CoV-2 community testing site (preprint)
Ford L , Whaley MJ , Shah MM , Salvatore PP , Segaloff HE , Delaney A , Currie DW , Boyle-Estheimer L , O'Hegarty M , Morgan CN , Meece J , Ivacic L , Thornburg NJ , Tamin A , Harcourt JL , Folster JM , Medrzycki M , Jain S , Wong P , Goffard K , Gieryn D , Kahrs J , Langolf K , Zochert T , Tate JE , Hsu CH , Kirking HL . medRxiv 2021 2021.07.06.21259792 Background Performance characteristics of SARS-CoV-2 antigen tests among children are limited despite the need for point-of-care testing in school and childcare settings. We describe children seeking SARS-CoV-2 testing at a community site and compare antigen test performance to real-time reverse transcription-polymerase chain reaction (RT-PCR) and viral culture.Methods Two anterior nasal specimens were self-collected for BinaxNOW antigen and RT-PCR testing, along with demographics, symptoms, and exposure information from individuals ≥5 years at a community testing site. Viral culture was attempted on residual antigen or RT-PCR positive specimens. Demographic and clinical characteristics, and the performance of SARS-CoV-2 antigen tests, were compared among children (<18 years) and adults.Results About one in ten included specimens were from children (225/2110); 16.4% (37/225) were RT-PCR positive. Cycle threshold values were similar among RT-PCR positive specimens from children and adults (22.5 vs 21.3, p=0.46) and among specimens from symptomatic and asymptomatic children (22.5 vs 23.2, p=0.39). Sensitivity of antigen test compared to RT-PCR was 73.0% (27/37) among specimens from children and 80.8% (240/297) among specimens from adults; among specimens from children, specificity was 100% (188/188), positive and negative predictive value were 100% (27/27) and 94.9% (188/198) respectively. Virus was isolated from 51.4% (19/37) of RT-PCR positive pediatric specimens; all 19 had positive antigen test results.Conclusions With lower sensitivity relative to RT-PCR, antigen tests may not diagnose all positive COVID-19 cases; however, antigen testing identified children with live SARS-CoV-2 virus.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThis work was supported by 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: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.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.YesThe datasets generated during and analyzed during the current study are available from the corresponding author on reasonable request. |
Adapterama II: Universal amplicon sequencing on Illumina platforms (TaggiMatrix) (preprint)
Glenn TC , Pierson TW , Bayona-Vásquez NJ , Kieran TJ , Hoffberg SL , Thomas IV JC , Lefever DE , Finger JW , Gao B , Bian X , Louha S , Kolli RT , Bentley KE , Rushmore J , Wong K , Shaw TI , Rothrock MJ Jr , McKee AM , Guo TL , Mauricio R , Molina M , Cummings BS , Lash LH , Lu K , Gilbert GS , Hubbell SP , Faircloth BC . bioRxiv 2019 619544 Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. Most NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In Adapterama I, we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5’ end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (eight forward primers + 12 reverse primers yield 8 × 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy. |
- Page last reviewed:Feb 1, 2024
- Page last updated:Apr 29, 2024
- Content source:
- Powered by CDC PHGKB Infrastructure