Last data update: Apr 29, 2024. (Total: 46658 publications since 2009)
Records 1-30 (of 62 Records) |
Query Trace: Hagen M [original query] |
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Race, ethnicity, and delayed time to COVID-19 testing among US health care workers
Baymon DE , Vakkalanka JP , Krishnadasan A , Mohr NM , Talan DA , Hagen MB , Wallace K , Harland KK , Aisiku IP , Hou PC . JAMA Netw Open 2024 7 (4) e245697 IMPORTANCE: Access to COVID-19 testing is critical to reducing transmission and supporting early treatment decisions; when made accessible, the timeliness of testing may also be an important metric in mitigating community spread of the infection. While disparities in transmission and outcomes of COVID-19 have been well documented, the extent of timeliness of testing and the association with demographic factors is unclear. OBJECTIVES: To evaluate demographic factors associated with delayed COVID-19 testing among health care personnel (HCP) during the COVID-19 pandemic. DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used data from the Preventing Emerging Infections Through Vaccine Effectiveness Testing study, a multicenter, test-negative, case-control vaccine effectiveness study that enrolled HCP who had COVID-19 symptoms and testing between December 2020 and April 2022. Data analysis was conducted from March 2022 to Junne 2023. EXPOSURE: Displaying COVID-19-like symptoms and polymerase chain reaction testing occurring from the first day symptoms occurred up to 14 days after symptoms occurred. MAIN OUTCOMES AND MEASURES: Variables of interest included patient demographics (sex, age, and clinical comorbidities) and COVID-19 characteristics (vaccination status and COVID-19 wave). The primary outcome was time from symptom onset to COVID-19 testing, which was defined as early testing (≤2 days) or delayed testing (≥3 days). Associations of demographic characteristics with delayed testing were measured while adjusting for clinical comorbidities, COVID-19 characteristics, and test site using multivariable modeling to estimate relative risks and 95% CIs. RESULTS: A total of 5551 HCP (4859 female [82.9%]; 1954 aged 25-34 years [35.2%]; 4233 non-Hispanic White [76.3%], 370 non-Hispanic Black [6.7%], and 324 non-Hispanic Asian [5.8%]) were included in the final analysis. Overall, 2060 participants (37.1%) reported delayed testing and 3491 (62.9%) reported early testing. Compared with non-Hispanic White HCP, delayed testing was higher among non-Hispanic Black HCP (adjusted risk ratio, 1.18; 95%CI, 1.10-1.27) and for non-Hispanic HCP of other races (adjusted risk ratio, 1.17; 95% CI, 1.03-1.33). Sex and age were not associated with delayed testing. Compared with clinical HCP with graduate degrees, all other professional and educational groups had significantly delayed testing. CONCLUSIONS AND RELEVANCE: In this cross-sectional study of HCP, compared with non-Hispanic White HCP and clinical HCP with graduate degrees, non-Hispanic Black HCP, non-Hispanic HCP of other races, and HCP all other professional and education backgrounds were more likely to have delayed COVID-19 testing. These findings suggest that time to testing may serve as a valuable metric in evaluating sociodemographic disparities in the response to COVID-19 and future health mitigation strategies. |
Assessment of weight gain in adult patients living with HIV receiving first-line dolutegravir-based or efavirenz-based ART regimens in routine care clinics in Tshwane district, South Africa: An observational study
Sawry S , Ayalew K , Maimela G , Briggs-Hagen M , van Wyk-Heath M , Mthethwa S , Shai S , Mngomezulu NN , Tlhowe L , Achere-Darko J , Bedford J , Martin CE , Fairlie L , Imrie J . HIV Med 2024 INTRODUCTION: Although dolutegravir (DTG) is deemed stable, safe, cost-effective, and clinically beneficial, it also carries the risk of side effects, including observed weight gain among patients on DTG-based antiretroviral therapy (ART) regimens. We compared weight changes among adults (≥18 years) initiating tenofovir disoproxil fumarate, lamivudine, and dolutegravir (TLD) or tenofovir disoproxil fumarate, emtricitabine, and efavirenz (TEE) regimens and those switching from TEE to TLD (TEE-to-TLD switchers) in three large primary care facilities in South Africa METHODS: We conducted a retrospective longitudinal record review using patient medical records, extracting relevant demographic and clinical data from October 2018 to June 2021 from randomly selected adults who initiated TLD or TEE (initiators) and adult TEE-to-TLD switchers. We assessed weight, body mass index (BMI), and percentage weight changes for both groups and fitted linear regression and generalized linear models to determine factors associated with weight and BMI change and percentage weight change ≥10%, respectively, among treatment initiators. We fitted linear mixed-effect models among TEE-to-TLD switchers to consider repeated measures. RESULTS: Of 860 initiators, 450 (52.3%) initiated on TEE and 410 (47.7%) on TLD, with median follow-up of 1.4 years and 1.0 year, respectively. At initiation, 43.3% on TEE and 40.8% on TLD were overweight or obese. TLD initiators had an adjusted higher mean weight gain of 1.6 kg (p < 0.001) and mean BMI gain of 0.51 kg/m(2) (p < 0.001) than TEE initiators. Independent risk factors for higher mean weight and BMI included age ≥50 years, male, on ART for >12 months, initial BMI of <18.5 kg/m(2), and CD4 counts <200 cells/μL. Of 298 TEE-to-TLD switchers, 36.6% were overweight or obese at TEE initiation. Comparing before and after TLD switch, TEE-to-TLD switchers had an adjusted mean weight of 1.2 kg less while on TLD (p = 0.026). Being overweight and CD4 counts >350 cells/μL were independent risk factors for lower weight gain after TLD switch. CONCLUSIONS: We report more weight gain among TLD than among TEE initiators, although to a lesser extent than previously reported. TEE-to-TLD switchers experienced less weight gain after TLD switch; return to health before receiving TLD may be a contributory factor. The current findings are reassuring for those switching to a DTG-based regimen. |
Clinical and laboratory characteristics of patients hospitalized with severe COVID-19 in New Orleans, August 2020 to September 2021
Drouin A , Plumb ID , McCullough M , James Gist J , Liu S , Theberge M , Katz J , Moreida M , Flaherty S , Chatwani B , Briggs Hagen M , Midgley CM , Fusco D . Sci Rep 2024 14 (1) 6539 Louisiana experienced high morbidity and mortality from COVID-19. To assess possible explanatory factors, we conducted a cohort study (ClinSeqSer) of patients hospitalized with COVID-19 in New Orleans during August 2020-September 2021. Following enrollment, we reviewed medical charts, and performed SARS-CoV-2 RT-PCR testing on nasal and saliva specimens. We used multivariable logistic regression to assess associations between patient characteristics and severe illness, defined as ≥ 6 L/min oxygen or intubation. Among 456 patients, median age was 56 years, 277 (60.5%) were Black non-Hispanic, 436 (95.2%) had underlying health conditions, and 358 were unvaccinated (92.0% of 389 verified). Overall, 187 patients (40.1%) had severe illness; 60 (13.1%) died during admission. In multivariable models, severe illness was associated with age ≥ 65 years (OR 2.08, 95% CI 1.22-3.56), hospitalization > 5 days after illness onset (OR 1.49, 95% CI 1.01-2.21), and SARS CoV-2 cycle threshold (Ct) result of < 32 in saliva (OR 4.79, 95% CI 1.22-18.77). Among patients who were predominantly Black non-Hispanic, unvaccinated and with underlying health conditions, approximately 1 in 3 patients had severe COVID-19. Older age and delayed time to admission might have contributed to high case-severity. An association between case-severity and low Ct value in saliva warrants further investigation. |
Differences in report of post-covid conditions among adults tested for SARS-cov-2 by race and ethnicity: 2022 Porter Novelli SummerStyles Survey, U.S
Feldstein LR , Edwards D , Cope JR , Hagen MB , Saydah S . AJPM Focus 2024 3 (2) 100181 INTRODUCTION: Since March 2020, Hispanic and Black/African American persons have made up a disproportionate number of COVID-19 cases, hospitalizations, and deaths. However, little is known about whether the prevalence of postacute sequelae or post-COVID conditions differs by race/ethnicity. METHODS: This study used cross-sectional survey data collected by Porter Novelli Public Services to determine the prevalence of ≥1 ongoing symptom lasting ≥4 weeks by SARS-CoV-2 test status and racial/ethnic groups among 2,890 adults in the U.S. RESULTS: Overall, 57% (95% CI=54%, 60%) of respondents with positive SARS-CoV-2 tests reported ≥1 ongoing symptom, compared with 22% (95% CI=20%, 24%) of respondents who tested negative. Among those with positive SARS-CoV-2 tests, Hispanic respondents had higher AORs of experiencing ≥1 ongoing symptom (AOR=1.79, 95% CI=1.27, 2.53) than non-Hispanic White respondents. In addition, Hispanic respondents had significantly higher ORs of experiencing 2 or more ongoing symptoms (AOR=2.03, 95% CI=1.45, 2.86), respiratory/cardiac symptoms (AOR=1.47, 95% CI=1.03, 2.07), neurologic symptoms (AOR=1.77, 95% CI=1.26, 2.48), and other symptoms (AOR=1.53, 95% CI=1.09, 2.14) than non-Hispanic White respondents. Non-Hispanic other respondents who reported at least 1 positive SARS-CoV-2 test had significantly higher ORs of experiencing gastrointestinal symptoms (AOR=4.06, 95% CI=1.78, 8.89) than non-Hispanic White respondents. CONCLUSIONS: These results highlight potential disparities in ongoing symptoms, even after accounting for demographic differences, and reinforce the need for culturally appropriate and targeted strategies to increase access to health care and reduce SARS-CoV-2 infections. |
Ethnic and racial differences in self-reported symptoms, health status, activity level, and missed work at 3 and 6 months following SARS-CoV-2 infection
O'Laughlin KN , Klabbers RE , Ebna Mannan I , Gentile NL , Geyer RE , Zheng Z , Yu H , Li SX , Chan KCG , Spatz ES , Wang RC , L'Hommedieu M , Weinstein RA , Plumb ID , Gottlieb M , Huebinger RM , Hagen M , Elmore JG , Hill MJ , Kelly M , McDonald S , Rising KL , Rodriguez RM , Venkatesh A , Idris AH , Santangelo M , Koo K , Saydah S , Nichol G , Stephens KA . Front Public Health 2023 11 1324636 INTRODUCTION: Data on ethnic and racial differences in symptoms and health-related impacts following SARS-CoV-2 infection are limited. We aimed to estimate the ethnic and racial differences in symptoms and health-related impacts 3 and 6 months after the first SARS-CoV-2 infection. METHODS: Participants included adults with SARS-CoV-2 infection enrolled in a prospective multicenter US study between 12/11/2020 and 7/4/2022 as the primary cohort of interest, as well as a SARS-CoV-2-negative cohort to account for non-SARS-CoV-2-infection impacts, who completed enrollment and 3-month surveys (N = 3,161; 2,402 SARS-CoV-2-positive, 759 SARS-CoV-2-negative). Marginal odds ratios were estimated using GEE logistic regression for individual symptoms, health status, activity level, and missed work 3 and 6 months after COVID-19 illness, comparing each ethnicity or race to the referent group (non-Hispanic or white), adjusting for demographic factors, social determinants of health, substance use, pre-existing health conditions, SARS-CoV-2 infection status, COVID-19 vaccination status, and survey time point, with interactions between ethnicity or race and time point, ethnicity or race and SARS-CoV-2 infection status, and SARS-CoV-2 infection status and time point. RESULTS: Following SARS-CoV-2 infection, the majority of symptoms were similar over time between ethnic and racial groups. At 3 months, Hispanic participants were more likely than non-Hispanic participants to report fair/poor health (OR: 1.94; 95%CI: 1.36-2.78) and reduced activity (somewhat less, OR: 1.47; 95%CI: 1.06-2.02; much less, OR: 2.23; 95%CI: 1.38-3.61). At 6 months, differences by ethnicity were not present. At 3 months, Other/Multiple race participants were more likely than white participants to report fair/poor health (OR: 1.90; 95% CI: 1.25-2.88), reduced activity (somewhat less, OR: 1.72; 95%CI: 1.21-2.46; much less, OR: 2.08; 95%CI: 1.18-3.65). At 6 months, Asian participants were more likely than white participants to report fair/poor health (OR: 1.88; 95%CI: 1.13-3.12); Black participants reported more missed work (OR, 2.83; 95%CI: 1.60-5.00); and Other/Multiple race participants reported more fair/poor health (OR: 1.83; 95%CI: 1.10-3.05), reduced activity (somewhat less, OR: 1.60; 95%CI: 1.02-2.51; much less, OR: 2.49; 95%CI: 1.40-4.44), and more missed work (OR: 2.25; 95%CI: 1.27-3.98). DISCUSSION: Awareness of ethnic and racial differences in outcomes following SARS-CoV-2 infection may inform clinical and public health efforts to advance health equity in long-term outcomes. |
Effectiveness of bivalent mRNA COVID-19 vaccines in preventing SARS-cov-2 infection in children and adolescents aged 5 to 17 years
Feldstein LR , Britton A , Grant L , Wiegand R , Ruffin J , Babu TM , Briggs Hagen M , Burgess JL , Caban-Martinez AJ , Chu HY , Ellingson KD , Englund JA , Hegmann KT , Jeddy Z , Lauring AS , Lutrick K , Martin ET , Mathenge C , Meece J , Midgley CM , Monto AS , Newes-Adeyi G , Odame-Bamfo L , Olsho LEW , Phillips AL , Rai RP , Saydah S , Smith N , Steinhardt L , Tyner H , Vandermeer M , Vaughan M , Yoon SK , Gaglani M , Naleway AL . Jama 2024 331 (5) 408-416 IMPORTANCE: Bivalent mRNA COVID-19 vaccines were recommended in the US for children and adolescents aged 12 years or older on September 1, 2022, and for children aged 5 to 11 years on October 12, 2022; however, data demonstrating the effectiveness of bivalent COVID-19 vaccines are limited. OBJECTIVE: To assess the effectiveness of bivalent COVID-19 vaccines against SARS-CoV-2 infection and symptomatic COVID-19 among children and adolescents. DESIGN, SETTING, AND PARTICIPANTS: Data for the period September 4, 2022, to January 31, 2023, were combined from 3 prospective US cohort studies (6 sites total) and used to estimate COVID-19 vaccine effectiveness among children and adolescents aged 5 to 17 years. A total of 2959 participants completed periodic surveys (demographics, household characteristics, chronic medical conditions, and COVID-19 symptoms) and submitted weekly self-collected nasal swabs (irrespective of symptoms); participants submitted additional nasal swabs at the onset of any symptoms. EXPOSURE: Vaccination status was captured from the periodic surveys and supplemented with data from state immunization information systems and electronic medical records. MAIN OUTCOME AND MEASURES: Respiratory swabs were tested for the presence of the SARS-CoV-2 virus using reverse transcriptase-polymerase chain reaction. SARS-CoV-2 infection was defined as a positive test regardless of symptoms. Symptomatic COVID-19 was defined as a positive test and 2 or more COVID-19 symptoms within 7 days of specimen collection. Cox proportional hazards models were used to estimate hazard ratios for SARS-CoV-2 infection and symptomatic COVID-19 among participants who received a bivalent COVID-19 vaccine dose vs participants who received no vaccine or monovalent vaccine doses only. Models were adjusted for age, sex, race, ethnicity, underlying health conditions, prior SARS-CoV-2 infection status, geographic site, proportion of circulating variants by site, and local virus prevalence. RESULTS: Of the 2959 participants (47.8% were female; median age, 10.6 years [IQR, 8.0-13.2 years]; 64.6% were non-Hispanic White) included in this analysis, 25.4% received a bivalent COVID-19 vaccine dose. During the study period, 426 participants (14.4%) had laboratory-confirmed SARS-CoV-2 infection. Among these 426 participants, 184 (43.2%) had symptomatic COVID-19, 383 (89.9%) were not vaccinated or had received only monovalent COVID-19 vaccine doses (1.38 SARS-CoV-2 infections per 1000 person-days), and 43 (10.1%) had received a bivalent COVID-19 vaccine dose (0.84 SARS-CoV-2 infections per 1000 person-days). Bivalent vaccine effectiveness against SARS-CoV-2 infection was 54.0% (95% CI, 36.6%-69.1%) and vaccine effectiveness against symptomatic COVID-19 was 49.4% (95% CI, 22.2%-70.7%). The median observation time after vaccination was 276 days (IQR, 142-350 days) for participants who received only monovalent COVID-19 vaccine doses vs 50 days (IQR, 27-74 days) for those who received a bivalent COVID-19 vaccine dose. CONCLUSION AND RELEVANCE: The bivalent COVID-19 vaccines protected children and adolescents against SARS-CoV-2 infection and symptomatic COVID-19. These data demonstrate the benefit of COVID-19 vaccine in children and adolescents. All eligible children and adolescents should remain up to date with recommended COVID-19 vaccinations. |
Opportunities to monitor disparities in asthma and other respiratory diseases using public health data
Sircar K , Hagen MB , Prezzato E , Hsu J . Ann Allergy Asthma Immunol 2023 131 (6) 683-684 In the United States, asthma and chronic obstructive pulmonary disease (COPD) affect approximately 8% and 6% of people, respectively.1,2 Certain populations are disproportionately affected. For instance, asthma prevalence is higher among people who are non-Hispanic (NH) Black or have lower incomes3; COPD is more prevalent among individuals with less than a high school education.2 | | Early in the COVID-19 pandemic, National Syndromic Surveillance Program data showed reduced overall, asthma-, and COPD-related emergency department (ED) visits in 2020 compared with 2019.1 Less is known about how decreases in asthma- and COPD–related emergency healthcare use (eg, ED visits, hospitalizations) varied across communities by demographics including race, ethnicity, and income. |
Effectiveness of a bivalent mRNA vaccine dose against symptomatic SARS-CoV-2 infection among U.S. Healthcare personnel, September 2022-May 2023
Plumb ID , Briggs Hagen M , Wiegand R , Dumyati G , Myers C , Harland KK , Krishnadasan A , James Gist J , Abedi G , Fleming-Dutra KE , Chea N , Lee JE , Kellogg M , Edmundson A , Britton A , Wilson LE , Lovett SA , Ocampo V , Markus TM , Smithline HA , Hou PC , Lee LC , Mower W , Rwamwejo F , Steele MT , Lim SC , Schrading WA , Chinnock B , Beiser DG , Faine B , Haran JP , Nandi U , Chipman AK , LoVecchio F , Eucker S , Femling J , Fuller M , Rothman RE , Curlin ME , Talan DA , Mohr NM . Vaccine 2023 BACKGROUND: Bivalent mRNA vaccines were recommended since September 2022. However, coverage with a recent vaccine dose has been limited, and there are few robust estimates of bivalent VE against symptomatic SARS-CoV-2 infection (COVID-19). We estimated VE of a bivalent mRNA vaccine dose against COVID-19 among eligible U.S. healthcare personnel who had previously received monovalent mRNA vaccine doses. METHODS: We conducted a case-control study in 22 U.S. states, and enrolled healthcare personnel with COVID-19 (case-participants) or without COVID-19 (control-participants) during September 2022-May 2023. Participants were considered eligible for a bivalent mRNA dose if they had received 2-4 monovalent (ancestral-strain) mRNA vaccine doses, and were ≥67 days after the most recent vaccine dose. We estimated VE of a bivalent mRNA dose using conditional logistic regression, accounting for matching by region and four-week calendar period. We adjusted estimates for age group, sex, race and ethnicity, educational level, underlying health conditions, community COVID-19 exposure, prior SARS-CoV-2 infection, and days since the last monovalent mRNA dose. RESULTS: Among 3,647 healthcare personnel, 1,528 were included as case-participants and 2,119 as control-participants. Participants received their last monovalent mRNA dose a median of 404 days previously; 1,234 (33.8%) also received a bivalent mRNA dose a median of 93 days previously. Overall, VE of a bivalent dose was 34.1% (95% CI, 22.6%-43.9%) against COVID-19 and was similar by product, days since last monovalent dose, number of prior doses, age group, and presence of underlying health conditions. However, VE declined from 54.8% (95% CI, 40.7%-65.6%) after 7-59 days to 21.6% (95% CI 5.6%-34.9%) after ≥60 days. CONCLUSIONS: Bivalent mRNA COVID-19 vaccines initially conferred approximately 55% protection against COVID-19 among U.S. healthcare personnel. However, protection waned after two months. These findings indicate moderate initial protection against symptomatic SARS-CoV-2 infection by remaining up-to-date with COVID-19 vaccines. |
Effectiveness of a messenger RNA vaccine booster dose against coronavirus disease 2019 among US healthcare personnel, October 2021-July 2022
Plumb ID , Mohr NM , Hagen M , Wiegand R , Dumyati G , Harland KK , Krishnadasan A , Gist JJ , Abedi G , Fleming-Dutra KE , Chea N , Lee J , Barter D , Brackney M , Fridkin SK , Wilson LE , Lovett SA , Ocampo V , Phipps EC , Marcus TM , Smithline HA , Hou PC , Lee LC , Moran GJ , Krebs E , Steele MT , Lim SC , Schrading WA , Chinnock B , Beiser DG , Faine B , Haran JP , Nandi U , Chipman AK , LoVecchio F , Talan DA , Pilishvili T . Open Forum Infect Dis 2023 10 (10) ofad457 BACKGROUND: Protection against symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (coronavirus disease 2019 [COVID-19]) can limit transmission and the risk of post-COVID conditions, and is particularly important among healthcare personnel. However, lower vaccine effectiveness (VE) has been reported since predominance of the Omicron SARS-CoV-2 variant. METHODS: We evaluated the VE of a monovalent messenger RNA (mRNA) booster dose against COVID-19 from October 2021 to June 2022 among US healthcare personnel. After matching case-participants with COVID-19 to control-participants by 2-week period and site, we used conditional logistic regression to estimate the VE of a booster dose compared with completing only 2 mRNA doses >150 days previously, adjusted for multiple covariates. RESULTS: Among 3279 case-participants and 3998 control-participants who had completed 2 mRNA doses, we estimated that the VE of a booster dose against COVID-19 declined from 86% (95% confidence interval, 81%-90%) during Delta predominance to 65% (58%-70%) during Omicron predominance. During Omicron predominance, VE declined from 73% (95% confidence interval, 67%-79%) 14-60 days after the booster dose, to 32% (4%-52%) ≥120 days after a booster dose. We found that VE was similar by age group, presence of underlying health conditions, and pregnancy status on the test date, as well as among immunocompromised participants. CONCLUSIONS: A booster dose conferred substantial protection against COVID-19 among healthcare personnel. However, VE was lower during Omicron predominance, and waning effectiveness was observed 4 months after booster dose receipt during this period. Our findings support recommendations to stay up to date on recommended doses of COVID-19 vaccines for all those eligible. |
Recommendations for setting a criterion and assessing commutability of sample materials used in external quality assessment/proficiency testing schemes
Sandberg S , Fauskanger P , Johansen JV , Keller T , Budd J , Greenberg N , Rej R , Panteghini M , Delatour V , Ceriotti F , Deprez L , Camara JE , MacKenzie F , Lyle AN , van der Hagen E , Burns C , Greg Miller W . Clin Chem 2023 69 (11) 1227-1237 It is important for external quality assessment materials (EQAMs) to be commutable with clinical samples; i.e., they should behave like clinical samples when measured using end-user clinical laboratory in vitro diagnostic medical devices (IVD-MDs). Using commutable EQAMs makes it possible to evaluate metrological traceability and/or equivalence of results between IVD-MDs. The criterion for assessing commutability of an EQAM between 2 IVD-MDs is that its result should be within the prediction interval limits based on the statistical distribution of the clinical sample results from the 2 IVD-MDs being compared. The width of the prediction interval is, among other things, dependent on the analytical performance characteristics of the IVD-MDs. A presupposition for using this criterion is that the differences in nonselectivity between the 2 IVD-MDs being compared are acceptable. An acceptable difference in nonselectivity should be small relative to the analytical performance specifications used in the external quality assessment scheme. The acceptable difference in nonselectivity is used to modify the prediction interval criterion for commutability assessment. The present report provides recommendations on how to establish a criterion for acceptable commutability for EQAMS, establish the difference in nonselectivity that can be accepted between IVD-MDs, and perform a commutability assessment. The report also contains examples for performing a commutability assessment of EQAMs. |
Viral determinants of acute COVID-19 symptoms in a nonhospitalized adult population in the pre-Omicron era
Goldberg SA , Lu S , Garcia-Knight M , Davidson MC , Tassetto M , Anglin K , Pineda-Ramirez J , Chen JY , Rugart PR , Mathur S , Forman CA , Donohue KC , Abedi GR , Saydah S , Briggs-Hagen M , Midgley CM , Andino R , Peluso MJ , Glidden DV , Martin JN , Kelly JD . Open Forum Infect Dis 2023 10 (8) ofad396 BACKGROUND: The influence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA level and presence of infectious virus on symptom occurrence is poorly understood, particularly among nonhospitalized individuals. METHODS: The study included 85 nonhospitalized, symptomatic adults, who were enrolled from September 2020 to November 2021. Data from a longitudinal cohort studied over 28 days was used to analyze the association of individual symptoms with SARS-CoV-2 viral RNA load, or the presence or level of infectious (culturable) virus. Presence of infectious virus and viral RNA load were assessed daily, depending on specimen availability, and amount of infectious virus was assessed on the day of maximum RNA load. Participants were surveyed for the start and end dates of 31 symptoms at enrollment and at days 9, 14, 21, and 28; daily symptom presence was determined analytically. We describe symptoms and investigate their possible association with viral determinants through a series of single or pooled (multiple days across acute period) cross-sectional analyses. RESULTS: There was an association between viral RNA load and the same-day presence of many individual symptoms. Additionally, individuals with infectious virus were more than three times as likely to have a concurrent fever than individuals without infectious virus, and more than two times as likely to have concurrent myalgia, chills, headache, or sore throat. CONCLUSIONS: We found evidence to support the association of viral RNA load and infectious virus on some, but not all symptoms. Fever was most strongly associated with the presence of infectious virus; this may support the potential for symptom-based isolation guidance for COVID-19. |
Recommendations for setting a criterion for assessing commutability of secondary calibrator certified reference materials
Miller WG , Keller T , Budd J , Johansen JV , Panteghini M , Greenberg N , Delatour V , Ceriotti F , Deprez L , Rej R , Camara JE , MacKenzie F , Lyle AN , van der Hagen E , Burns C , Fauskanger P , Sandberg S . Clin Chem 2023 69 (9) 966-975 A secondary higher-order calibrator is required to be commutable with clinical samples to be suitable for use in the calibration hierarchy of an end-user clinical laboratory in vitro diagnostic medical device (IVD-MD). Commutability is a property of a reference material that means results for a reference material and for clinical samples have the same numeric relationship, within specified limits, across the measurement procedures for which the reference material is intended to be used. Procedures for assessing commutability have been described in the literature. This report provides recommendations for establishing a quantitative criterion to assess the commutability of a certified reference material (CRM). The criterion is the maximum allowable noncommutability bias (MANCB) that allows a CRM to be used as a calibrator in a calibration hierarchy for an IVD-MD without exceeding the maximum allowable combined standard uncertainty for a clinical sample result (umaxCS). Consequently, the MANCB is derived as a fraction of the umaxCS for the measurand. The suitability of an MANCB for practical use in a commutability assessment is determined by estimating the number of measurements of clinical samples and CRMs required based on the precision performance and nonselectivity for the measurand of the measurement procedures in the assessment. Guidance is also provided for evaluating indeterminate commutability conclusions and how to report results of a commutability assessment. |
CASCADIA: a prospective community-based study protocol for assessing SARS-CoV-2 vaccine effectiveness in children and adults using a remote nasal swab collection and web-based survey design
Babu TM , Feldstein LR , Saydah S , Acker Z , Boisvert CL , Briggs-Hagen M , Carone M , Casto A , Cox SN , Ehmen B , Englund JA , Fortmann SP , Frivold CJ , Groom H , Han PD , Kuntz JL , Lockwood T , Midgley CM , Mularski RA , Ogilvie T , Reich SL , Schmidt MA , Smith N , Starita L , Stone J , Vandermeer M , Weil AA , Wolf CR , Chu HY , Naleway AL . BMJ Open 2023 13 (7) e071446 INTRODUCTION: Although SARS-CoV-2 vaccines were first approved under Emergency Use Authorization by the Food and Drug Administration in late 2020 for adults, authorisation for young children 6 months to <5 years of age did not occur until 2022. These authorisations were based on clinical trials, understanding real-world vaccine effectiveness (VE) in the setting of emerging variants is critical. The primary goal of this study is to evaluate SARS-CoV-2 VE against infection among children aged >6 months and adults aged <50 years. METHODS: CASCADIA is a 4-year community-based prospective study of SARS-CoV-2 VE among 3500 adults and paediatric populations aged 6 months to 49 years in Oregon and Washington, USA. At enrolment and regular intervals, participants complete a sociodemographic questionnaire. Individuals provide a blood sample at enrolment and annually thereafter, with optional blood draws every 6 months and after infection and vaccination. Participants complete weekly self-collection of anterior nasal swabs and symptom questionnaires. Swabs are tested for SARS-CoV-2 and other respiratory pathogens by reverse transcription-PCR, with results of selected pathogens returned to participants; nasal swabs with SARS-CoV-2 detected will undergo whole genome sequencing. Participants who test positive for SARS-CoV-2 undergo serial swab collection every 3 days for 21 days. Serum samples are tested for SARS-CoV-2 antibody by binding and neutralisation assays. ANALYSIS: The primary outcome is SARS-CoV-2 infection. Cox regression models will be used to estimate the incidence rate ratio associated with SARS-CoV-2 vaccination among the paediatric and adult population, controlling for demographic factors and other potential confounders. ETHICS AND DISSEMINATION: All study materials including the protocol, consent forms, data collection instruments, participant communication and recruitment materials, were approved by the Kaiser Permanente Interregional Institutional Review Board, the IRB of record for the study. Results will be disseminated through peer-reviewed publications, presentations, participant newsletters and appropriate general news media. |
Longitudinal and Quantitative Fecal Shedding Dynamics of SARS-CoV-2, Pepper Mild Mottle Virus and CrAssphage (preprint)
Arts PJ , Kelly JD , Midgley CM , Anglin K , Lu S , Abedi GR , Andino R , Bakker KM , Banman B , Boehm AB , Briggs-Hagen M , Brouwer AF , Davidson MC , Eisenberg MC , Garcia-Knight M , Knight S , Peluso MJ , Pineda-Ramirez J , Sanchez RD , Saydah S , Tassetto M , Martin JN , Wigginton KR . medRxiv 2023 07 e0013223 Wastewater-based epidemiology (WBE) emerged during the COVID-19 pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden, though the lack of high-quality, longitudinal fecal shedding data of SARS-CoV-2 and other viruses limits the interpretation and applicability of wastewater measurements. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as the commonly used fecal indicators Pepper Mild Mottle Virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. The shedding trajectories from 48 SARS-CoV-2 infected individuals suggest a highly individualized, dynamic course of SARS-CoV-2 RNA fecal shedding, with individual measurements varying from below limit of detection to 2.79x106 gene copies/mg - dry mass of stool (gc/mg-dw). Of individuals that contributed at least 3 samples covering a range of at least 15 of the first 30 days after initial acute symptom onset, 77.4% had at least one positive SARS-CoV-2 RNA stool sample measurement. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall; and measured crAssphage DNA above detection limits in 80% (38/48) of individuals and 48% (179/371) of samples. Median shedding values for PMMoV and crAssphage nucleic acids were 1x105 gc/mg-dw and 1.86x103 gc/mgdw, respectively. These results can be used to inform and build mechanistic models to significantly broaden the potential of WBE modeling and to provide more accurate insight into SARS-CoV-2 prevalence estimates. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. |
CASCADIA: A prospective community-based study protocol for assessing SARS-CoV-2 vaccine effectiveness in children and adults utilizing a remote nasal swab collection and web-based survey design (preprint)
Babu TM , Feldstein LR , Saydah S , Acker Z , Boisvert CL , Briggs-Hagen M , Carone M , Casto A , Cox SN , Ehmen B , Englund JA , Fortmann SP , Frivold CJ , Groom H , Han P , Kuntz JL , Lockwood T , Midgley CM , Mularski RA , Ogilvie T , Reich S , Schmidt MA , Smith N , Starita L , Stone J , Vandermeer M , Weil AA , Wolf CR , Chu HY , Naleway AL . medRxiv 2023 07 Introduction: Although SARS-CoV-2 vaccines were first approved under Emergency Use Authorization by the FDA in late 2020 for adults, approval for young children 6 months to < 5 years of age did not occur until 2022. Understanding real world vaccine effectiveness in the setting of emerging variants is critical. The primary goal of this study is to evaluate SARS-CoV-2 vaccine effectiveness (VE) against infection among children aged >6 months and adults aged <50 years. Method(s): CASCADIA is a four-year community-based prospective study of SARS-CoV-2 VE among adult and pediatric populations aged 6 months to 49 years in Oregon and Washington. At enrollment and regular intervals, participants complete a sociodemographic questionnaire. Individuals provide a blood sample at enrollment and annually thereafter, with additional, optional blood draws after infection and vaccination. Participants complete weekly self-collection of anterior nasal swabs and symptom questionnaires. Swabs are tested for SARS-CoV-2 and other respiratory pathogens by RT-PCR, with results of selected pathogens returned to participants; nasal swabs with SARS-CoV-2 detected will undergo whole genome sequencing. Participants who report symptoms outside of their weekly swab collection and symptom survey are asked to collect an additional swab. Participants who test positive for SARS-CoV-2 undergo serial swab collection every three days for three weeks. Serum samples are tested for SARS-CoV-2 antibody by binding and neutralization assays. Analysis: Cox regression models will be used to estimate the hazard ratio associated with SARS-CoV-2 vaccination among the pediatric and adult population, controlling for demographic factors and potential confounders, including clustering within households. Ethics and dissemination: All study materials including the protocol, consent forms, participant communication and recruitment materials, and data collection instruments were approved by the Kaiser Permanente Northwest (KPNW) Institutional Review Board, the IRB of record for the study. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Presence of Symptoms 6 Weeks After COVID-19 Among Vaccinated and Unvaccinated U.S. Healthcare Personnel (preprint)
Mohr NM , Plumb ID , Harland KK , Pilishvili T , Fleming-Dutra KE , Krishnadasan A , Hoth KF , Saydah SH , Mankoff Z , Haran JP , Leon ES , Talan DA , Smithline HA , Hou PC , Lee LC , Lim SC , Moran GJ , Steele MT , Beiser DG , Faine B , Nandi U , Schrading WA , Chinnock B , Chipman A , Fuentes M , LoVecchio F , Clinansmith B , Landers S , Horcher A , Wallace K , Uribe L , Pathmarajah K , Poronsky KE , Hashimoto DM , Bahamon M , Romain MSt , Kean E , Krebs E , Stubbs A , Roy S , Volturo G , Higgins A , Galbraith J , Crosby JC , Mulrow M , Gonzalez E , Gierke R , Farrar JL , Xing W , Chung Y , Yousaf A , Okaro JO , Briggs-Hagen M , Abedi GR , Nyanseor S , Watts CK . medRxiv 2022 25 Importance: Although COVID-19 vaccines protect against infection and severe disease, the role of vaccination in preventing prolonged symptoms in those with subsequent infection is unclear. Objective(s): To determine differences in symptoms stratified by prior vaccination reported by healthcare personnel (HCP) 6 weeks after onset of COVID-19, and whether there were differences in timing of return to work. Design(s): Nested cohort study within a multicenter vaccine effectiveness study. HCP with COVID-19 between December 2020 and August 2021 were followed up 6 weeks after illness onset. Setting(s): Health systems in 12 U.S. states. Participant(s): HCP participating in a vaccine effectiveness study were eligible for inclusion if they had confirmed COVID-19 with either verified mRNA vaccination (symptom onset =14 days after two doses) or no prior COVID-19 vaccination. Among 681 eligible participants, 419 (61%) completed a follow-up survey approximately 6 weeks after illness onset. Exposures: Two doses of a COVID-19 mRNA vaccine compared with no COVID-19 vaccine. Main Outcomes and Measures: Presence of symptoms 6 weeks after onset of COVID-19 illness and days to return to work after COVID-19 illness. Result(s): Among 419 HCP with confirmed COVID-19, 298 (71%) reported one or more COVID-like symptoms 6 weeks after illness onset, with a lower prevalence among vaccinated participants (60.6%) compared with unvaccinated participants (60.6% vs. 79.1%; aRR 0.70, 95% CI 0.58-0.84). Vaccinated HCP returned to work a median 2.0 days (95% CI 1.0-3.0) sooner than unvaccinated HCP (aHR 1.37; 95% CI, 1.04-1.79). Conclusion(s): A history of two doses of COVID-19 mRNA vaccine among HCP with COVID-19 illness was associated with decreased risk of COVID-like symptoms at 6 weeks and earlier to return to work. Vaccination is associated with improved recovery from COVID-19, in addition to preventing symptomatic infection. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. |
Infectious viral shedding of SARS-CoV-2 Delta following vaccination: a longitudinal cohort study (preprint)
Garcia-Knight M , Anglin K , Tassetto M , Lu S , Zhang A , Goldberg SA , Catching A , Davidson MC , Shak JR , Romero M , Pineda-Ramirez J , Sanchez RD , Rugart P , Donohue K , Massachi J , Sans HM , Djomaleu M , Mathur S , Servellita V , McIlwain D , Gaudiliere B , Chen J , Martinez EO , Tavs JM , Bronstone G , Weiss J , Watson JT , Briggs-Hagen M , Abedi GR , Rutherford GW , Deeks SG , Chiu C , Saydah S , Peluso MJ , Midgley CM , Martin JN , Andino R , Kelly JD . medRxiv 2022 19 (9) e1010802 The impact of vaccination on SARS-CoV-2 infectiousness is not well understood. We compared longitudinal viral shedding dynamics in unvaccinated and fully vaccinated adults. SARS-CoV-2-infected adults were enrolled within 5 days of symptom onset and nasal specimens were self-collected daily for two weeks and intermittently for an additional two weeks. SARS-CoV-2 RNA load and infectious virus were analyzed relative to symptom onset stratified by vaccination status. We tested 1080 nasal specimens from 52 unvaccinated adults enrolled in the pre-Delta period and 32 fully vaccinated adults with predominantly Delta infections. While we observed no differences by vaccination status in maximum RNA levels, maximum infectious titers and the median duration of viral RNA shedding, the rate of decay from the maximum RNA load was faster among vaccinated; maximum infectious titers and maximum RNA levels were highly correlated. Furthermore, amongst participants with infectious virus, median duration of infectious virus detection was reduced from 7.5 days (IQR: 6.0-9.0) in unvaccinated participants to 6 days (IQR: 5.0-8.0) in those vaccinated (P=0.02). Accordingly, the odds of shedding infectious virus from days 6 to 12 post-onset were lower among vaccinated participants than unvaccinated participants (OR 0.42 95% CI 0.19-0.89). These results indicate that vaccination had reduced the probability of shedding infectious virus after 5 days from symptom onset. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. |
Trends in laboratory-confirmed SARS-CoV-2 reinfections and associated hospitalizations and deaths among adults aged 18 years - 18 U.S. Jurisdictions, September 2021-December 2022
Ma KC , Dorabawila V , León TM , Henry H , Johnson AG , Rosenberg E , Mansfield JA , Midgley CM , Plumb ID , Aiken J , Khanani QA , Auche S , Bayoumi NS , Bennett SA , Bernu C , Chang C , Como-Sabetti KJ , Cueto K , Cunningham S , Eddy M , Falender RA , Fleischauer A , Frank DM , Harrington P , Hoskins M , Howsare A , Ingaiza LM , Islam AS , Jensen SA , Jones JM , Kambach G , Kanishka F , Levin Y , Masarik JF 3rd , Meyer SD , Milroy L , Morris KJ , Olmstead J , Olsen NS , Omoike E , Patel K , Pettinger A , Pike MA , Reed IG , Slocum E , Sutton M , Tilakaratne BP , Vest H , Vostok J , Wang JS , Watson-Lewis L , Wienkes HN , Hagen MB , Silk BJ , Scobie HM . MMWR Morb Mortal Wkly Rep 2023 72 (25) 683-689 Although reinfections with SARS-CoV-2 have occurred in the United States with increasing frequency, U.S. epidemiologic trends in reinfections and associated severe outcomes have not been characterized. Weekly counts of SARS-CoV-2 reinfections, total infections, and associated hospitalizations and deaths reported by 18 U.S. jurisdictions during September 5, 2021-December 31, 2022, were analyzed overall, by age group, and by five periods of SARS-CoV-2 variant predominance (Delta and Omicron [BA.1, BA.2, BA.4/BA.5, and BQ.1/BQ.1.1]). Among reported reinfections, weekly trends in the median intervals between infections and frequencies of predominant variants during previous infections were calculated. As a percentage of all infections, reinfections increased substantially from the Delta (2.7%) to the Omicron BQ.1/BQ.1.1 (28.8%) periods; during the same periods, increases in the percentages of reinfections among COVID-19-associated hospitalizations (from 1.9% [Delta] to 17.0% [Omicron BQ.1/BQ.1.1]) and deaths (from 1.2% [Delta] to 12.3% [Omicron BQ.1/BQ.1.1]) were also substantial. Percentages of all COVID-19 cases, hospitalizations, and deaths that were reinfections were consistently higher across variant periods among adults aged 18-49 years compared with those among adults aged ≥50 years. The median interval between infections ranged from 269 to 411 days by week, with a steep decline at the start of the BA.4/BA.5 period, when >50% of reinfections occurred among persons previously infected during the Alpha variant period or later. To prevent severe COVID-19 outcomes, including those following reinfection, CDC recommends staying up to date with COVID-19 vaccination and receiving timely antiviral treatments, when eligible. |
Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage
Arts PJ , Kelly JD , Midgley CM , Anglin K , Lu S , Abedi GR , Andino R , Bakker KM , Banman B , Boehm AB , Briggs-Hagen M , Brouwer AF , Davidson MC , Eisenberg MC , Garcia-Knight M , Knight S , Peluso MJ , Pineda-Ramirez J , Diaz Sanchez R , Saydah S , Tassetto M , Martin JN , Wigginton KR . mSphere 2023 8 (4) e0013223 Wastewater-based epidemiology (WBE) emerged during the coronavirus disease 2019 (COVID-19) pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden. The lack of high-resolution fecal shedding data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) limits our ability to link WBE measurements to disease burden. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as for the commonly used fecal indicators pepper mild mottle virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. The shedding trajectories from 48 SARS-CoV-2-infected individuals suggest a highly individualized, dynamic course of SARS-CoV-2 RNA fecal shedding. Of the individuals that provided at least three stool samples spanning more than 14 days, 77% had one or more samples that tested positive for SARS-CoV-2 RNA. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall. CrAssphage DNA was detected in at least one sample from 80% (38/48) of individuals and was detected in 48% (179/371) of all samples. The geometric mean concentrations of PMMoV and crAssphage in stool across all individuals were 8.7 × 10(4) and 1.4 × 10(4) gene copies/milligram-dry weight, respectively, and crAssphage shedding was more consistent for individuals than PMMoV shedding. These results provide us with a missing link needed to connect laboratory WBE results with mechanistic models, and this will aid in more accurate estimates of COVID-19 burden in sewersheds. Additionally, the PMMoV and crAssphage data are critical for evaluating their utility as fecal strength normalizing measures and for source-tracking applications. IMPORTANCE This research represents a critical step in the advancement of wastewater monitoring for public health. To date, mechanistic materials balance modeling of wastewater-based epidemiology has relied on SARS-CoV-2 fecal shedding estimates from small-scale clinical reports or meta-analyses of research using a wide range of analytical methodologies. Additionally, previous SARS-CoV-2 fecal shedding data have not contained sufficient methodological information for building accurate materials balance models. Like SARS-CoV-2, fecal shedding of PMMoV and crAssphage has been understudied to date. The data presented here provide externally valid and longitudinal fecal shedding data for SARS-CoV-2, PMMoV, and crAssphage which can be directly applied to WBE models and ultimately increase the utility of WBE. |
Estimates of SARS-CoV-2 seroprevalence and incidence of primary SARS-CoV-2 infections among blood donors, by COVID-19 vaccination status - United States, April 2021-September 2022
Jones JM , Manrique IM , Stone MS , Grebe E , Saa P , Germanio CD , Spencer BR , Notari E , Bravo M , Lanteri MC , Green V , Briggs-Hagen M , Coughlin MM , Stramer SL , Opsomer J , Busch MP . MMWR Morb Mortal Wkly Rep 2023 72 (22) 601-605 Changes in testing behaviors and reporting requirements have hampered the ability to estimate the U.S. SARS-CoV-2 incidence (1). Hybrid immunity (immunity derived from both previous infection and vaccination) has been reported to provide better protection than that from infection or vaccination alone (2). To estimate the incidence of infection and the prevalence of infection- or vaccination-induced antibodies (or both), data from a nationwide, longitudinal cohort of blood donors were analyzed. During the second quarter of 2021 (April-June), an estimated 68.4% of persons aged ≥16 years had infection- or vaccination-induced SARS-CoV-2 antibodies, including 47.5% from vaccination alone, 12.0% from infection alone, and 8.9% from both. By the third quarter of 2022 (July-September), 96.4% had SARS-CoV-2 antibodies from previous infection or vaccination, including 22.6% from infection alone and 26.1% from vaccination alone; 47.7% had hybrid immunity. Prevalence of hybrid immunity was lowest among persons aged ≥65 years (36.9%), the group with the highest risk for severe disease if infected, and was highest among those aged 16-29 years (59.6%). Low prevalence of infection-induced and hybrid immunity among older adults reflects the success of public health infection prevention efforts while also highlighting the importance of older adults staying up to date with recommended COVID-19 vaccination, including at least 1 bivalent dose.*(,)(†). |
Comparing genomic variant identification protocols for Candida auris
Li X , Muñoz JF , Gade L , Argimon S , Bougnoux ME , Bowers JR , Chow NA , Cuesta I , Farrer RA , Maufrais C , Monroy-Nieto J , Pradhan D , Uehling J , Vu D , Yeats CA , Aanensen DM , d'Enfert C , Engelthaler DM , Eyre DW , Fisher MC , Hagen F , Meyer W , Singh G , Alastruey-Izquierdo A , Litvintseva AP , Cuomo CA . Microb Genom 2023 9 (4) Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35 Candida auris isolates from 4 distinct clades and evaluated the performance of variant calling, single-nucleotide polymorphism (SNP) counts and phylogenetic inference results. Although these pipelines used different variant callers and filtering criteria, we found high overall agreement of SNPs from each pipeline. This concordance correlated with site quality, as SNPs discovered by a few pipelines tended to show lower mapping quality scores and depth of coverage than those recovered by all pipelines. We observed that the major differences between pipelines were due to variation in read trimming strategies, SNP calling methods and parameters, and downstream filtration criteria. We calculated specificity and sensitivity for each pipeline by aligning three isolates with chromosomal level assemblies and found that the GATK-based pipelines were well balanced between these metrics. Selection of trimming methods had a greater impact on SAMtools-based pipelines than those using GATK. Phylogenetic trees inferred by each pipeline showed high consistency at the clade level, but there was more variability between isolates from a single outbreak, with pipelines that used more stringent cutoffs having lower resolution. This project generated two truth datasets useful for routine benchmarking of C. auris variant calling, a consensus VCF of genotypes discovered by 10 or more pipelines across these 35 diverse isolates and variants for 2 samples identified from whole-genome alignments. This study provides a foundation for evaluating SNP calling pipelines and developing best practices for future fungal genomic studies. |
Use of severe acute respiratory syndrome coronavirus 2 antibody tests by US infectious disease physicians: Results of an emerging infections network survey, March 2022
Gundlapalli AV , Beekmann SE , Jones JM , Thornburg NJ , Clarke KEN , Uyeki TM , Satheshkumar PS , Carroll DS , Plumb ID , Briggs-Hagen M , Santibañez S , David-Ferdon C , Polgreen PM , McDonald LC . Open Forum Infect Dis 2023 10 (3) ofad091 BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody tests have had limited recommended clinical application during the coronavirus disease 2019 (COVID-19) pandemic. To inform clinical practice, an understanding is needed of current perspectives of United States-based infectious disease (ID) physicians on the use, interpretation, and need for SARS-CoV-2 antibody tests. METHODS: In March 2022, members of the Emerging Infections Network (EIN), a national network of practicing ID physicians, were surveyed on types of SARS-CoV-2 antibody assays ordered, interpretation of test results, and clinical scenarios for which antibody tests were considered. RESULTS: Of 1867 active EIN members, 747 (40%) responded. Among the 583 who managed or consulted on COVID-19 patients, a majority (434/583 [75%]) had ordered SARS-CoV-2 antibody tests and were comfortable interpreting positive (452/578 [78%]) and negative (405/562 [72%]) results. Antibody tests were used for diagnosing post-COVID-19 conditions (61%), identifying prior SARS-CoV-2 infection (60%), and differentiating prior infection and response to COVID-19 vaccination (37%). Less than a third of respondents had used antibody tests to assess need for additional vaccines or risk stratification. Lack of sufficient evidence for use and nonstandardized assays were among the most common barriers for ordering tests. Respondents indicated that statements from professional societies and government agencies would influence their decision to order SARS-CoV-2 antibody tests for clinical decision making. CONCLUSIONS: Practicing ID physicians are using SARS-CoV-2 antibody tests, and there is an unmet need for clarifying the appropriate use of these tests in clinical practice. Professional societies and US government agencies can support clinicians in the community through the creation of appropriate guidance. |
School-based interventions to increase student COVID-19 vaccination coverage in public school populations with low coverage - Seattle, Washington, December 2021-June 2022
Fairlie T , Chu B , Thomas ES , Querns AK , Lyons A , Koziol M , Englund JA , Anderson EM , Graff K , Rigel S , Bell TR , Saydah S , Chatham-Stephens K , Vogt TM , Hoag S , Briggs-Hagen M . MMWR Morb Mortal Wkly Rep 2023 72 (11) 283-287 COVID-19 can lead to severe outcomes in children (1). Vaccination decreases risk for COVID-19 illness, severe disease, and death (2). On December 13, 2020, CDC recommended COVID-19 vaccination for persons aged ≥16 years, with expansion on May 12, 2021, to children and adolescents (children) aged 12-15 years, and on November 2, 2021, to children aged 5-11 years (3). As of March 8, 2023, COVID-19 vaccination coverage among school-aged children remained low nationwide, with 61.7% of children aged 12-17 years and approximately one third (32.7%) of those aged 5-11 years having completed the primary series (3). Intention to receive COVID-19 vaccine and vaccination coverage vary by demographic characteristics, including race and ethnicity and socioeconomic status (4-6). Seattle Public Schools (SPS) implemented a program to increase COVID-19 vaccination coverage during the 2021-22 school year, focusing on children aged 5-11 years during November 2021-June 2022, with an added focus on populations with low vaccine coverage during January 2022-June 2022.(†) The program included strategic messaging, school-located vaccination clinics, and school-led community engagement. Vaccination data from the Washington State Immunization Information System (WAIIS) were analyzed to examine disparities in COVID-19 vaccination by demographic and school characteristics and trends over time. In December 2021, 56.5% of all SPS students, 33.7% of children aged 5-11 years, and 81.3% of children aged 12-18 years had completed a COVID-19 primary vaccination series. By June 2022, overall series completion had increased to 80.3% and was 74.0% and 86.6% among children aged 5-11 years and 12-18 years, respectively. School-led vaccination programs can leverage community partnerships and relationships with families to improve COVID-19 vaccine access and coverage. |
Protection from COVID-19 mRNA vaccination and prior SARS-CoV-2 infection against COVID-19-associated encounters in adults during Delta and Omicron predominance.
Bozio CH , Butterfield KA , Briggs Hagen M , Grannis S , Drawz P , Hartmann E , Ong TC , Fireman B , Natarajan K , Dascomb K , Gaglani M , DeSilva MB , Yang DH , Midgley CM , Dixon BE , Naleway AL , Grisel N , Liao IC , Reese SE , Fadel WF , Irving SA , Lewis N , Arndorfer J , Murthy K , Riddles J , Valvi NR , Mamawala M , Embi PJ , Thompson MG , Stenehjem E . J Infect Dis 2023 227 (12) 1348-1363 BACKGROUND: Data assessing protection conferred from COVID-19 mRNA vaccination and/or prior SARS-CoV-2 infection during Delta and Omicron predominance periods in the U.S. are limited. METHODS: This cohort study included persons ≥18 years who had ≥1 healthcare encounter across four health systems and had been tested for SARS-CoV-2 before August 26, 2021. COVID-19 mRNA vaccination and prior SARS-CoV-2 infection defined the exposure. Cox regression estimated hazard ratios (HRs) for the Delta and Omicron periods; protection was calculated as (1-HR)x100%. RESULTS: Compared to unvaccinated and previously uninfected persons, during Delta predominance, protection against COVID-19-associated hospitalizations was high for those 2- or 3-dose vaccinated and previously infected, 3-dose vaccinated alone, and prior infection alone (range:91%-97%, with overlapping 95% confidence intervals (95%CIs)); during Omicron predominance, estimates were lower (range:77%-90%). Protection against COVID-19-associated emergency department/urgent care (ED/UC) encounters during Delta predominance was high for those exposure groups (range:86%-93%); during Omicron predominance, protection remained high for those 3-dose vaccinated with or without a prior infection (76% (95%CI=67%-83%) and 71% (95%CI=67%-73%), respectively). CONCLUSIONS: COVID-19 mRNA vaccination and/or prior SARS-CoV-2 infection provided protection against COVID-19-associated hospitalizations and ED/UC encounters regardless of variant. Staying up-to-date with COVID-19 vaccination still provides protection against severe COVID-19 disease, regardless of prior infection. |
Prevalence of and risk factors for human immunodeficiency virus (HIV) infection in entrants and residents of an Ethiopian prison
Sahle ET , Amogne W , Manyazewal T , Blumenthal J , Jain S , Sun S , Young J , Ellorin E , Woldeamanuel H , Teferra L , Feleke B , Vandenberg O , Rey Z , Briggs-Hagen M , Haubrich R , McCutchan JA . PLoS One 2023 18 (2) e0271666 BACKGROUND: Prisoners generally have a higher prevalence of HIV infection compared to the general population from which they come. Whether this higher prevalence reflects a higher HIV prevalence in those entering prisons or intramural transmission of HIV within prisons or both is unclear. Any of these possibilities would increase the prevalence found in resident prisoners above that in the general population. Moreover, comparisons of HIV prevalence in entrants and residents and in men and women in African prisons are not well documented. The purpose of this study was to estimate and compare the prevalence and risk factors for HIV infection amongst both male as well as female and entrant and resident prisoners in a large Ethiopian Federal Prison. METHODS: We studied consenting prisoners cross-sectionally from August 2014 through November 2016. Prison entrants were screened continuously for HIV infection and its associated risk factors and residents were screened in two waves one year apart. HIV was diagnosed at the prison hospital laboratory based on the Ethiopian national HIV rapid antibody testing protocol. An external, internationally-accredited reference laboratory confirmed results. Agreement of results between the laboratories were assessed. RESULTS: A total of 10,778 participants were screened for HIV. Most participants were young (median age of 26 years, IQR: 21-33), male (84%), single (61%), literate (89%), and urban residents (91%) without prior incarceration (96%). Prevalence of HIV was 3.4% overall. Rates of HIV (p = 0.80) were similar in residents and entrants in wave 1 and in entrants in both waves, but were 1.9-fold higher (5.4% vs 2.8%) in residents than entrants in wave 2 (both p<0.001). At entrance to the prison women were more likely to be HIV+ than men (5.5% in women vs 2.5% in men, p< 0.001). In contrast resident women were less likely to be HIV+, but this difference was not statistically significant (3.2% in women vs 4.3% in men, p = 0.125). Other risk factors associated with HIV infection were increasing age (p<0.001), female gender (p<0.001), marital status (never vs other categories, p = 0.016), smaller number of rooms in their houses pre-imprisonment (p = 0.031), TB diagnosis ever (p<0.001), number of lifetime sex partners (especially having 2-10, p<0.001), and genital ulcer (p = 0.037). CONCLUSIONS: Prevalence of HIV in the residents at this large, central Ethiopian prison was higher than that estimated for the general population and lower than in many other studies from other smaller Ethiopian prisons. A higher prevalence in residents than in entrants were found only in our second wave of screening after one year of continuous screening and treatment, possibly representing increased willingness of residents at increased risk of HIV to participate in the second wave. Thus, this findings did not clearly support intramural transmission of HIV or the effectiveness of screening to reduce prevalence. Finally, the higher HIV prevalence in women than men requires that they be similarly screened and treated for HIV infection. |
Use of epidemiology surge support to enhance robustness and expand capacity of SARS-CoV-2 pandemic response, South Africa
Taback-Esra R , Morof D , Briggs-Hagen M , Savva H , Mthethwa S , Williams D , Drummond J , Rothgerber N , Smith M , McMorrow M , Ndlovu M , Adelekan A , Kindra G , Olivier J , Mpofu N , Motlhaoleng K , Khuzwayo L , Makapela D , Manjengwa P , Ochieng A , Porter S , Grund J , Diallo K , Lacson R . Emerg Infect Dis 2022 28 (13) S177-s180 As COVID-19 cases increased during the first weeks of the pandemic in South Africa, the National Institute of Communicable Diseases requested assistance with epidemiologic and surveillance expertise from the US Centers for Disease Control and Prevention South Africa. By leveraging its existing relationship with the National Institute of Communicable Diseases for >2 months, the US Centers for Disease Control and Prevention South Africa supported data capture and file organization, data quality reviews, data analytics, laboratory strengthening, and the development and review of COVID-19 guidance This case study provides an account of the resources and the technical, logistical, and organizational capacity leveraged to support a rapid response to the COVID-19 pandemic in South Africa. |
Presence of symptoms 6 weeks after COVID-19 among vaccinated and unvaccinated US healthcare personnel: a prospective cohort study
Mohr NM , Plumb ID , Harland KK , Pilishvili T , Fleming-Dutra KE , Krishnadasan A , Hoth KF , Saydah SH , Mankoff Z , Haran JP , Briggs-Hagen M , León ES , Talan DA . BMJ Open 2023 13 (2) e063141 OBJECTIVES: Although COVID-19 vaccines offer protection against infection and severe disease, there is limited information on the effect of vaccination on prolonged symptoms following COVID-19. Our objective was to determine differences in prevalence of prolonged symptoms 6 weeks after onset of COVID-19 among healthcare personnel (HCP) by vaccination status, and to assess differences in timing of return to work. DESIGN: Cohort analysis of HCP with COVID-19 enrolled in a multicentre vaccine effectiveness study. HCP with COVID-19 between December 2020 and August 2021 were followed up 6 weeks after illness onset. SETTING: Health systems in 12 US states. PARTICIPANTS: HCP participating in a vaccine effectiveness study were eligible for inclusion if they had laboratory-confirmed symptomatic SARS-CoV-2 with mRNA vaccination (symptom onset ≥14 days after two doses) or no prior vaccination. Among 681 eligible participants, 419 (61%) completed a follow-up survey to assess symptoms reported 6 weeks after illness onset. EXPOSURES: Two doses of a COVID-19 mRNA vaccine compared with no COVID-19 vaccine. MAIN OUTCOME MEASURES: Prevalence of symptoms 6 weeks after onset of COVID-19 illness and days to return to work. RESULTS: Among 419 HCP with COVID-19, 298 (71%) reported one or more COVID-like symptoms 6 weeks after illness onset, with a lower prevalence among vaccinated participants compared with unvaccinated participants (60.6% vs 79.1%; adjusted risk ratio 0.70, 95% CI 0.58 to 0.84). Following their illness, vaccinated HCP returned to work a median 2.0 days (95% CI 1.0 to 3.0) sooner than unvaccinated HCP (adjusted HR 1.37, 95% CI 1.04 to 1.79). CONCLUSIONS: Receipt of two doses of a COVID-19 mRNA vaccine among HCP with COVID-19 illness was associated with decreased prevalence of COVID-like symptoms at 6 weeks and earlier return to work. |
Association of culturable-virus detection and household transmission of SARS-CoV-2 - California and Tennessee, 2020-2022
Deyoe JE , Kelly JD , Grijalva CG , Bonenfant G , Lu S , Anglin K , Garcia-Knight M , Pineda-Ramirez J , Briggs Hagen M , Saydah S , Abedi GR , Goldberg SA , Tassetto M , Zhang A , Donohue KC , Davidson MC , Diaz Sanchez R , Djomaleu M , Mathur S , Shak JR , Deeks SG , Peluso MJ , Chiu CY , Zhu Y , Halasa NB , Chappell JD , Mellis A , Reed C , Andino R , Martin JN , Zhou B , Talbot HK , Midgley CM , Rolfes MA . J Infect Dis 2023 From two SARS-CoV-2 household transmission studies (enrolling April 2020 - January 2022) with rapid enrollment and specimen collection for 14 days, 61% (43/70) of primary cases had culturable-virus detected ≥6 days post-onset. Risk of secondary infection among household contacts tended to be greater when primary cases had culturable-virus detected after onset. Regardless of duration of culturable-virus, most secondary infections [70% (28/40)] had serial intervals <6 days, suggesting early transmission. These data examine viral culture as a proxy for infectiousness, reaffirm the need for rapid control measures after infection and highlight the potential for prolonged infectiousness (≥6 days) in many individuals. |
Development of a mobile app to increase uptake of HIV pre-exposure prophylaxis among latino sexual minority men: A qualitative needs assessment
Cantos VD , Hagen KS , Duarte AP , Escobar C , Batina I , Orozco H , Rodriguez J , Camacho-Gonzalez AF , Siegler AJ . JMIR Form Res 2023 7 e43844 BACKGROUND: Latino sexual minority men (SMM) are disproportionally impacted by HIV. Uptake of pre-exposure prophylaxis (PrEP), an effective biomedical intervention to prevent HIV acquisition, is low in this group compared to White SMM. Mobile technology (mHealth) represents an innovative strategy to increase PrEP uptake among Latino SMM. OBJECTIVE: This paper describes the qualitative process that led to the development of SaludFindr, a comprehensive HIV prevention mobile app that aims to increase PrEP uptake, HIV testing, and condom use by Latino SMM. METHODS: We conducted 13 in-depth interviews with Latino SMM living in metropolitan Atlanta to explore the main barriers and facilitators to PrEP uptake in this group and analyze their overall opinions of potential SaludFindr app functionalities. To explore potential app functions, we used HealthMindr, an existing comprehensive HIV prevention app, as a template and added new proposed features intended to address the specific needs of this community. RESULTS: We identified general PrEP uptake barriers that, although common among non-Latino groups, had added complexities such as the influence of religion and family on stigma. Low perceived PrEP eligibility, intersectional stigma, lack of insurance, cost concerns, and misconceptions about PrEP side effects, were described as general barriers. We also identified Latino-specific barriers that predominantly hinder access to existing services, including a scarcity of PrEP clinics that are prepared to provide culturally-concordant services, limited availability of Spanish-language written information related to PrEP access, distrust of peers as credible sources of information, perceived ineligibility for low-cost services due to undocumented status, fear of immigration authorities, and competing work obligations that prevent PrEP clinic attendance. Healthcare providers represented a trusted source of information and three provider characteristics were identified as PrEP facilitators: familiarity prescribing PrEP, being Latino, and being part of LGBTQIA+ or ally. The proposed app was very well accepted, with particularly high interest in features that facilitate PrEP access, including a tailored list of clinics that meet the community needs and a private platform where app users can gather reliable PrEP information. Spanish language availability and free or low-cost PrEP care represented the two main clinic criteria that would facilitate PrEP uptake. Latino representation in clinic staff and providers, perception of the clinic as a "safe-space" for undocumented patients, and LGBTQIA+ representation were listed as additional criteria. Only 8 our of the 47 clinics listed on PrEP locator.org for the Atlanta area fulfilled at least the two main criteria. CONCLUSIONS: This study provides further evidence of the significant barriers to PrEP uptake that Latino SMM face, exposes the urgent need to increase the number of accessible PrEP-providing clinics for Latino SMM, and proposes an innovative, community-driven, and mobile technology-based tool as a future intervention to overcome some of those barriers. |
Paxlovid Associated with Decreased Hospitalization Rate Among Adults with COVID-19 - United States, April-September 2022.
Shah MM , Joyce B , Plumb ID , Sahakian S , Feldstein LR , Barkley E , Paccione M , Deckert J , Sandmann D , Gerhart JL , Hagen MB . MMWR Morb Mortal Wkly Rep 2022 71 (48) 1531-1537 Nirmatrelvir-ritonavir (Paxlovid), an oral antiviral treatment, is authorized for adults with mild-to-moderate COVID-19 who are at increased risk for progression to severe illness. However, real-world evidence on the benefit of Paxlovid, according to vaccination status, age group, and underlying health conditions, is limited. To examine the benefit of Paxlovid in adults aged ≥18 years in the United States, a large electronic health record (EHR) data set (Cosmos(†)) was analyzed to assess the association between receiving a prescription for Paxlovid and hospitalization with a COVID-19 diagnosis in the ensuing 30 days. A Cox proportional hazards model was used to estimate this association, adjusted for demographic characteristics, geographic location, vaccination, previous infection, and number of underlying health conditions. Among 699,848 adults aged ≥18 years eligible for Paxlovid during April-August 2022, 28.4% received a Paxlovid prescription within 5 days of COVID-19 diagnosis. Being prescribed Paxlovid was associated with a lower hospitalization rate among the overall study population (adjusted hazard ratio [aHR] = 0.49), among those who had received ≥3 mRNA COVID-19 vaccines (aHR = 0.50), and across age groups (18-49 years: aHR = 0.59; 50-64 years: aHR = 0.40; and ≥65 years: aHR = 0.53). Paxlovid should be prescribed to eligible adults to reduce the risk of COVID-19-associated hospitalization. |
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