Risk of Subsequent Respiratory Virus Detection After Primary Virus Detection in a Community Household Study-King County, Washington, 2019-2021.

BACKGROUND: The epidemiology of respiratory viral infections is complex. How infection with one respiratory virus affects risk of subsequent infection with the same or another respiratory virus is not well described. METHODS: From October 2019 to June 2021, enrolled households completed active surveillance for acute respiratory illness (ARI), and participants with ARI self-collected nasal swab specimens; after April 2020, participants with ARI or laboratory-confirmed severe acute respiratory syndrome coronavirus 2 and their household members self-collected nasal swab specimens. Specimens were tested using multiplex reverse-transcription polymerase chain reaction for respiratory viruses. A Cox regression model with a time-dependent covariate examined risk of subsequent detections following a specific primary viral detection. RESULTS: Rhinovirus was the most frequently detected pathogen in study specimens (406 [9.5%]). Among 51 participants with multiple viral detections, rhinovirus to seasonal coronavirus (8 [14.8%]) was the most common viral detection pairing. Relative to no primary detection, there was a 1.03-2.06-fold increase in risk of subsequent virus detection in the 90 days after primary detection; risk varied by primary virus: human parainfluenza virus, rhinovirus, and respiratory syncytial virus were statistically significant. CONCLUSIONS: Primary virus detection was associated with higher risk of subsequent virus detection within the first 90 days after primary detection.

Simultaneous measurement of orthogonal terahertz fields via an emission multiplexing scheme.

We propose a polarization sensitive terahertz time-domain spectrometer that can record orthogonally polarized terahertz fields simultaneously, using fibre-coupled photoconductive antennas and a scheme that modulated the emitter's polarization. The s and p channels of the multi-pixel terahertz emitter were modulated at different frequencies, thereby allowing orthogonal waveforms to be demultiplexed from the recorded signal in post-processing. The performance of the multi-pixel emitter used in this multiplexing scheme was comparable to that of a commercial single-polarization H-dipole antenna. The approach allowed two orthogonally polarized terahertz pulses to be recorded with good signal to noise (>1000:1) within half a second. We verified the capability of the spectrometer by characterizing a birefringent crystal and by imaging a polarization-sensitive metamaterial. This work has significant potential to improve the speed of terahertz polarization sensitive applications, such as ellipsometry and imaging.

Determinants of Type-Specific Human Papillomavirus Concordance Across Anatomic Sites in Young Men Who Have Sex With Men and Transgender Women, 3 U.S. Cities, 2016-2018.

BACKGROUND: Among men who have sex with men (MSM) and transgender women (TGW), the dynamics of human papillomavirus (HPV) infections at different anatomical sites are not well understood. Information on HPV concordance between anatomic sites can inform the extent of autoinoculation, and susceptibility of different anatomic areas to HPV infection. We described and assessed correlates of HPV concordance across anal, oral, and genital samples. METHODS: We enrolled 1876 MSM and TGW aged 18 to 26 years in 3 US cities. Oral, genital, and anal samples were self-collected for type-specific HPV DNA testing (37 types). Demographics, sexual behaviors, and health history were self-reported. Kappa statistics based on percent positive agreement (kappa+) and generalized estimating equations were used to describe and identify correlates of HPV type-specific concordance between anatomic sample pairs. RESULTS: Any HPV was detected in 69.9%, 48.6%, and 7.4% of anal, genital, and oral samples, respectively. Detection of any HPV (concurrence) was most common in anal-genital pairs (40.9%) and uncommon in oral-genital and oral-anal pairs (3.4% and 6.5% respectively). Type-specific concordance was poor across all sample pairs (kappa+ <0.20). Younger age and older age at first sex were positively associated with type-concordant anal-genital infections. Sexual behaviors were unassociated with concordance. CONCLUSIONS: Poor oral/anogenital concordance suggests the oral mucosa has different susceptibility to HPV infection, differential clearance and/or autoinoculation between oral and anogenital sites is unlikely. There was some observed concurrence and concordance between anal and genital sites, unassociated with sexual behavior, suggesting autoinoculation. Longitudinal studies are necessary to further elucidate mechanisms of multisite infections.

The Relationship Between Insertive Oral and Anal Sex and Select Measures of the Composition of the Urethral Microbiota Among Men Who Have Sex With Men.

BACKGROUND: Sexual behavior may influence the composition of the male urethral microbiota, but this hypothesis has not been tested in longitudinal studies of men who have sex with men (MSM). METHODS: From December 2014 to July 2018, we enrolled MSM with nongonococcal urethritis (NGU) attending a sexual health clinic. Men attended 5 in-clinic visits at 3-week intervals, collected weekly urine specimens at home, and reported daily antibiotics and sexual activity on weekly diaries. We applied broad-range 16S rRNA gene sequencing to urine. We used generalized estimating equations to estimate the association between urethral sexual exposures in the prior 7 days (insertive oral sex [IOS] only, condomless insertive anal intercourse [CIAI] only, IOS with CIAI [IOS + CIAI], or none) and Shannon index, number of species (observed, oral indicator, and rectal indicator), and specific taxa, adjusting for recent antibiotics, age, race/ethnicity, HIV, and preexposure prophylaxis. RESULTS: Ninety-six of 108 MSM with NGU attended ≥1 follow-up visit. They contributed 1140 person-weeks of behavioral data and 1006 urine specimens. Compared with those with no urethral sexual exposures, those with IOS only had higher Shannon index ( P = 0.03 ) but similar number of species and presence of specific taxa considered, adjusting for confounders; the exception was an association with Haemophilus parainfluenzae . CIAI only was not associated with measured aspects of the urethral microbiota. IOS + CIAI was only associated with presence of H. parainfluenzae and Haemophilus . CONCLUSIONS: Among MSM after NGU, IOS and CIAI did not seem to have a substantial influence on measured aspects of the composition of the urethral microbiota.

Robust analysis of stepped wedge trials using composite likelihood models.

Stepped wedge trials (SWTs) are a type of cluster randomized trial that involve repeated measures on clusters and design-induced confounding between time and treatment. Although mixed models are commonly used to analyze SWTs, they are susceptible to misspecification particularly for cluster-longitudinal designs such as SWTs. Mixed model estimation leverages both "horizontal" or within-cluster information and "vertical" or between-cluster information. To use horizontal information in a mixed model, both the mean model and correlation structure must be correctly specified or accounted for, since time is confounded with treatment and measurements are likely correlated within clusters. Alternative non-parametric methods have been proposed that use only vertical information; these are more robust because between-cluster comparisons in a SWT preserve randomization, but these non-parametric methods are not very efficient. We propose a composite likelihood method that focuses on vertical information, but has the flexibility to recover efficiency by using additional horizontal information. We compare the properties and performance of various methods, using simulations based on COVID-19 data and a demonstration of application to the LIRE trial. We found that a vertical composite likelihood model that leverages baseline data is more robust than traditional methods, and more efficient than methods that use only vertical information. We hope that these results demonstrate the potential value of model-based vertical methods for SWTs with a large number of clusters, and that these new tools are useful to researchers who are concerned about misspecification of traditional models.

Remote surveillance and detection of SARS-CoV-2 transmission among household members in King County, Washington.

BACKGROUND: Early during the COVID-19 pandemic, it was important to better understand transmission dynamics of SARS-CoV-2, the virus that causes COVID-19. Household contacts of infected individuals are particularly at risk for infection, but delays in contact tracing, delays in testing contacts, and isolation and quarantine posed challenges to accurately capturing secondary household cases. METHODS: In this study, 346 households in the Seattle region were provided with respiratory specimen collection kits and remotely monitored using web-based surveys for respiratory illness symptoms weekly between October 1, 2020, and June 20, 2021. Symptomatic participants collected respiratory specimens at symptom onset and mailed specimens to the central laboratory in Seattle. Specimens were tested for SARS-CoV-2 using RT-PCR with whole genome sequencing attempted when positive. SARS-CoV-2-infected individuals were notified, and their household contacts submitted specimens every 2 days for 14 days. RESULTS: In total, 1371 participants collected 2029 specimens that were tested; 16 individuals (1.2%) within 6 households tested positive for SARS-CoV-2 during the study period. Full genome sequences were generated from 11 individuals within 4 households. Very little genetic variation was found among SARS-CoV-2 viruses sequenced from different individuals in the same household, supporting transmission within the household. CONCLUSIONS: This study indicates web-based surveillance of respiratory symptoms, combined with rapid and longitudinal specimen collection and remote contact tracing, provides a viable strategy to monitor households and detect household transmission of SARS-CoV-2. TRIAL REGISTRATION IDENTIFIER: NCT04141930, Date of registration 28/10/2019.

Changing genomic epidemiology of COVID-19 in long-term care facilities during the 2020-2022 pandemic, Washington State.

BACKGROUND: Long-term care facilities (LTCFs) are vulnerable to disease outbreaks. Here, we jointly analyze SARS-CoV-2 genomic and paired epidemiologic data from LTCFs and surrounding communities in Washington state (WA) to assess transmission patterns during 2020-2022, in a setting of changing policy. We describe sequencing efforts and genomic epidemiologic findings across LTCFs and perform in-depth analysis in a single county. METHODS: We assessed genomic data representativeness, built phylogenetic trees, and conducted discrete trait analysis to estimate introduction sizes over time, and explored selected outbreaks to further characterize transmission events. RESULTS: We found that transmission dynamics among cases associated with LTCFs in WA changed over the course of the COVID-19 pandemic, with variable introduction rates into LTCFs, but decreasing amplification within LTCFs. SARS-CoV-2 lineages circulating in LTCFs were similar to those circulating in communities at the same time. Transmission between staff and residents was bi-directional. CONCLUSIONS: Understanding transmission dynamics within and between LTCFs using genomic epidemiology on a broad scale can assist in targeting policies and prevention efforts. Tracking facility-level outbreaks can help differentiate intra-facility outbreaks from high community transmission with repeated introduction events. Based on our study findings, methods for routine tree building and overlay of epidemiologic data for hypothesis generation by public health practitioners are recommended. Discrete trait analysis added valuable insight and can be considered when representative sequencing is performed. Cluster detection tools, especially those that rely on distance thresholds, may be of more limited use given current data capture and timeliness. Importantly, we noted a decrease in data capture from LTCFs over time. Depending on goals for use of genomic data, sentinel surveillance should be increased or targeted surveillance implemented to ensure available data for analysis.

Prior Exposure to Azithromycin and Azithromycin Resistance Among Persons Diagnosed With Neisseria gonorrhoeae Infection at a Sexual Health Clinic: 2012-2019.

BACKGROUND: There is conflicting evidence on whether prior azithromycin (AZM) exposure is associated with reduced susceptibility to AZM (AZMRS) among persons infected with Neisseria gonorrhoeae (NG). METHODS: The study population included Public Health-Seattle and King County Sexual Health Clinic (SHC) patients with culture-positive NG infection at ≥1 anatomic site whose isolates were tested for AZM susceptibility in 2012-2019. We used multivariate logistic regression to examine the association of time since last AZM prescription from the SHC in ≤12 months with subsequent diagnosis with AZMRS NG (minimum inhibitory concentration [MIC], ≥2.0 µg/mL) and used linear regression to assess the association between the number of AZM prescriptions in ≤12 months and AZM MIC level, controlling for demographic, behavioral, and clinical characteristics. RESULTS: A total of 2155 unique patients had 2828 incident NG infections, 156 (6%) of which were caused by AZMRS NG. AZMRS NG was strongly associated with receipt of AZM from the SHC in the prior 29 days (adjusted odds ratio, 6.76; 95% confidence interval [CI], 1.76 to 25.90) but not with receipt of AZM in the prior 30-365 days. Log AZM MIC level was not associated with the number of AZM prescriptions within ≤12 months (adjusted correlation, 0.0004; 95% CI, -.04 to .037) but was associated with number of prescriptions within <30 days (adjusted coefficient, 0.56; 95% CI, .13 to .98). CONCLUSIONS: Recent individual-level AZM treatment is associated with subsequent AZMRS gonococcal infections. The long half-life and persistence of subtherapeutic levels of AZM may result in selection of resistant NG strains in persons with recent AZM use.

Tissue Washing Improves Native Ambient Mass Spectrometry Detection of Membrane Proteins Directly from Tissue.

Native ambient mass spectrometry enables the in situ analysis of proteins and their complexes directly from tissue, providing both structural and spatial information. Until recently, the approach was applied exclusively to the analysis of soluble proteins; however, there is a drive for new techniques that enable analysis of membrane proteins. Here we demonstrate native ambient mass spectrometry of membrane proteins, including ß-barrel and α-helical (single and multipass) integral membrane proteins and membrane-associated proteins incorporating lipid anchors, by integration of a simple washing protocol to remove soluble proteins. Mass spectrometry imaging revealed that washing did not disrupt the spatial distributions of the membrane and membrane-associated proteins. Some delocalization of the remaining soluble proteins was observed.

Sentinel Surveillance System Implementation and Evaluation for SARS-CoV-2 Genomic Data, Washington, USA, 2020-2021.

Genomic data provides useful information for public health practice, particularly when combined with epidemiologic data. However, sampling bias is a concern because inferences from nonrandom data can be misleading. In March 2021, the Washington State Department of Health, USA, partnered with submitting and sequencing laboratories to establish sentinel surveillance for SARS-CoV-2 genomic data. We analyzed available genomic and epidemiologic data during presentinel and sentinel periods to assess representativeness and timeliness of availability. Genomic data during the presentinel period was largely unrepresentative of all COVID-19 cases. Data available during the sentinel period improved representativeness for age, death from COVID-19, outbreak association, long-term care facility-affiliated status, and geographic coverage; timeliness of data availability and captured viral diversity also improved. Hospitalized cases were underrepresented, indicating a need to increase inpatient sampling. Our analysis emphasizes the need to understand and quantify sampling bias in phylogenetic studies and continue evaluation and improvement of public health surveillance systems.

Cabotegravir for the prevention of HIV-1 in women: results from HPTN 084, a phase 3, randomised clinical trial.

BACKGROUND: Oral pre-exposure prophylaxis has been introduced in more than 70 countries, including many in sub-Saharan Africa, but women experience considerable barriers to daily pill-taking, such as stigma, judgement, and the fear of violence. Safe and effective long-acting agents for HIV prevention are needed for women. We aimed to evaluate the safety and efficacy of injectable cabotegravir compared with daily oral tenofovir diphosphate plus emtricitabine (TDF-FTC) for HIV prevention in HIV-uninfected women. METHODS: HPTN 084 was a phase 3, randomised, double-blind, double-dummy, active-controlled, superiority trial in 20 clinical research sites in seven countries in sub-Saharan Africa. Participants were eligible for enrolment if they were assigned female sex at birth, were aged 18-45 years, reported at least two episodes of vaginal intercourse in the previous 30 days, were at risk of HIV infection based on an HIV risk score, and agreed to use a long-acting reversible contraceptive method. Participants were randomly assigned (1:1) to either active cabotegravir with TDF-FTC placebo (cabotegravir group) or active TDF-FTC with cabotegravir placebo (TDF-FTC group). Study staff and participants were masked to study group allocation, with the exception of the site pharmacist who was responsible for study product preparation. Participants were prescribed 5 weeks of daily oral product followed by intramuscular injections every 8 weeks after an initial 4-week interval load, alongside daily oral pills. Participants who discontinued injections were offered open-label daily TDF-FTC for 48 weeks. The primary endpoints of the study were incident HIV infection in the intention-to-treat population, and clinical and laboratory events that were grade 2 or higher in all women who had received at least one dose of study product. This study is registered with ClinicalTrials.gov, NCT03164564. FINDINGS: From Nov 27, 2017, to Nov 4, 2020, we enrolled 3224 participants (1614 in the cabotegravir group and 1610 in the TDF-FTC group). Median age was 25 years (IQR 22-30); 1755 (54·7%) of 3209 had two or more partners in the preceding month. 40 incident infections were observed over 3898 person-years (HIV incidence 1·0% [95% CI 0·73-1·40]); four in the cabotegravir group (HIV incidence 0·2 cases per 100 person-years [0·06-0·52]) and 36 in the TDF-FTC group (1·85 cases per 100 person-years [1·3-2·57]; hazard ratio 0·12 [0·05-0·31]; p<0·0001; risk difference -1·6% [-1·0% to -2·3%]. In a random subset of 405 TDF-FTC participants, 812 (42·1%) of 1929 plasma samples had tenofovir concentrations consistent with daily use. Injection coverage was 93% of the total number of person-years. Adverse event rates were similar across both groups, apart from injection site reactions, which were more frequent in the cabotegravir group than in the TDF-FTC group (577 [38·0%] of 1519 vs 162 [10·7%] of 1516]) but did not result in injection discontinuation. Confirmed pregnancy incidence was 1·3 per 100 person-years (0·9-1·7); no congenital birth anomalies were reported. INTERPRETATION: Although both products for HIV prevention were generally safe, well tolerated, and effective, cabotegravir was superior to TDF-FTC in preventing HIV infection in women. FUNDING: National Institute of Allergy and Infectious Diseases, ViiV Healthcare, and the Bill & Melinda Gates Foundation. Additional support was provided through the National Institute of Mental Health, the National Institute on Drug Abuse, and the Eunice Kennedy Shriver National Institute of Child Health and Human Development. ViiV Healthcare and Gilead Sciences provided pharmaceutical support.

Inadequate performance of a risk score to predict asymptomatic Neisseria gonorrhoeae and Chlamydia trachomatis infection among cisgender men who have sex with men.

OBJECTIVES: Epidemiological treatment of persons who are sexual contacts to partners with Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) often results in treatment of uninfected persons, which may increase the risk of antibiotic-resistant infections. We sought to identify the predictors of NG and/or CT infections to develop a risk score that could be used to limit epidemiological treatment to persons most likely to have these infections. METHODS: We included visits to the Public Health - Seattle & King County Sexual Health Clinic by asymptomatic cisgender men who have sex with men (MSM) aged ≥18 who presented as a sexual contact to partner(s) with CT or NG infection between 2011 and 2019. We used logistic regression to estimate the odds of CT and/or NG infections associated with demographic and clinical predictors, selecting the final set of predictors using the Akaike information criteria and obtaining score weights from model coefficients. We used a cross-validation approach to obtain average model discrimination from each of 10 models, leaving out 10% of the data, and evaluated sensitivity and specificity at various score cut-offs. RESULTS: The final model for predicting NG or CT infection included seven predictors (age <35 years, HIV status, receptive oral sex in the prior 2 months, CT diagnosis, condomless receptive anal intercourse, condomless insertive anal intercourse and methamphetamine use in the prior 12 months). Model discrimination, as measured by the receiver operating curve, was 0.60 (95% CI 0.54 to 0.66). Sensitivity for detection of infection was ≥90% for scores ≥3, ≥5 and ≥7; specificity for these cut-offs was <16%. At scores ≥9, ≥12 and ≥14, specificity increased but sensitivity decreased to ≤76%. CONCLUSIONS: Our risk score did not sufficiently discriminate between asymptomatic MSM with and without NG/CT infection. Additional studies evaluating epidemiological treatment as a standard of care in diverse populations are needed to guide best practices in the management of contacts to NG/CT infection.

Ultrafast THz spectroscopy of carbon nanotube-graphene composites.

Mixed nanomaterial composites can combine the excellent properties of well-known low-dimensional nanomaterials. Here we highlight the potential of one-dimensional single-walled carbon nanotubes interfaced with two-dimensional graphene by exploring the composite's ac conductivity and photoconductivity, and the influence of HAuCl4doping. In the composite, the equilibrium terahertz conductivity from free carrier motion was boosted, while the localised plasmon peak shifted towards higher frequencies, which we attribute to shorter conductivity pathways in the composite. A negative terahertz photoconductivity was observed for all samples under 410 nm optical excitation and was reproduced by a simple model, where the Drude spectral weight and the momentum scattering rate were both lowered under photoexcitation. The composite had an enhanced modulation depth in comparison to reference carbon nanotube films, while retaining their characteristically fast (picosecond) response time. The results show that carbon nanotube-graphene composites offer new opportunities in devices by controlling charge carrier transport and tuning their optoelectronic properties.

Incidence of SARS-CoV-2 infection and associated risk factors among staff and residents at homeless shelters in King County, Washington: an active surveillance study.

Homeless shelter residents and staff may be at higher risk of SARS-CoV-2 infection. However, SARS-CoV-2 infection estimates in this population have been reliant on cross-sectional or outbreak investigation data. We conducted routine surveillance and outbreak testing in 23 homeless shelters in King County, Washington, to estimate the occurrence of laboratory-confirmed SARS-CoV-2 infection and risk factors during 1 January 2020-31 May 2021. Symptom surveys and nasal swabs were collected for SARS-CoV-2 testing by RT-PCR for residents aged ≥3 months and staff. We collected 12,915 specimens from 2,930 unique participants. We identified 4.74 (95% CI 4.00-5.58) SARS-CoV-2 infections per 100 individuals (residents: 4.96, 95% CI 4.12-5.91; staff: 3.86, 95% CI 2.43-5.79). Most infections were asymptomatic at the time of detection (74%) and detected during routine surveillance (73%). Outbreak testing yielded higher test positivity than routine surveillance (2.7% versus 0.9%). Among those infected, residents were less likely to report symptoms than staff. Participants who were vaccinated against seasonal influenza and were current smokers had lower odds of having an infection detected. Active surveillance that includes SARS-CoV-2 testing of all persons is essential in ascertaining the true burden of SARS-CoV-2 infections among residents and staff of congregate settings.

Diverging Neisseria gonorrhoeae Morbidity in Non-Hispanic Black and White Females: Application of Group-Based Trajectory Modeling to Trends in County-Level Morbidity 2003-2018.

National trends in gonorrhea rates may obscure informative local variations in morbidity. We used group-based trajectory models to identify groups of counties with similar gonorrhea rate trajectories among non-Hispanic White (NHW) and non-Hispanic Black (NHB) females using county-level data on gonorrhea cases in US females from 2003 to 2018. We assessed models with 1-15 groups and selected final models based on fit statistics and identification of divergent trajectory groups with distinct intercepts and/or slopes. We mapped counties by assigned trajectory group and examined the association of county characteristics with group membership. We identified 7 distinct gonorrhea trajectory groups for NHW females and 9 distinct trajectory groups for NHB females. All identified groups for NHW female morbidity experienced increasing gonorrhea rates with a limited range (11.6-183.3/100,000 NHW females in 2018); trajectories of NHB female morbidity varied widely in rates (146.6-966.0/1000 NHB females in 2018) and included 3 groups of counties that experienced a net decline in gonorrhea rates. Counties with higher NHW female morbidity had lower adult sex ratios, lower health insurance coverage, and lower marital rates among NHW adults. Counties with higher NHB female morbidity were more urban, experienced higher rates of poverty, and had lower rates of marriage among NHB adults. Morbidity patterns did not always follow geographic proximity, which could be explained by variation in social determinants of health. Our results demonstrated a highly heterogenous gonorrhea epidemic among NHW and NHB US females, which should prompt further analysis into the differential drivers of gonorrhea morbidity.

The Incidence Rate of Sexual Behaviors Among Cisgender Men Who Have Sex with Men Attending a Sexual Health Clinic.

Although nuanced parameterization of sexual behavior may improve estimates from mathematical models of human immunodeficiency virus and sexually transmitted infection transmission, prospective estimates of the incidence of specific sexual behaviors among men who have sex with men (MSM) are limited. From December 2014 to July 2018, MSM with and without nongonococcal urethritis (NGU) completed weekly diaries over 3-12 weeks. Incidence rates of any sex, receptive anal sex, insertive anal sex, insertive oral sex, receptive rimming, and receptive hand-penile contact were 1.19, 0.28, 0.66, 0.90, 0.24, and 0.85 episodes per person-week, respectively, among 104 MSM with NGU at baseline, and 1.33, 0.54, 0.32, 0.95, 0.44, and 0.88 episodes per person-week, respectively, among 25 MSM without NGU at baseline. Most receptive anal sex (NGU + 83%, NGU - 86%) and insertive anal sex (NGU + 85%, NGU - 76%) episodes were condomless. MSM engaged in sex just over once per week, and condom use was infrequent. Insertive oral sex and receptive hand-penile contact were the most common behaviors.

Burden of long COVID among adults experiencing sheltered homelessness: a longitudinal cohort study in King County, WA between September 2020-April 2022.

BACKGROUND: People experiencing homelessness (PEH) are at increased risk for acquiring SARS-CoV-2, but the burden of long COVID in this population is unknown. METHODS: We conducted a matched prospective cohort study to assess the prevalence, characteristics, and impact of long COVID among sheltered PEH in Seattle, WA between September 2020-April 2022. Adults ≥ 18 years, residing across nine homeless shelters with active respiratory virus surveillance, were eligible to complete in-person baseline surveys and interval follow-up phone surveys. We included a subset of 22 COVID-19-positive cases who tested positive or inconclusive for SARS-CoV-2 and 44 COVID-19-negative controls who tested negative for SARS-CoV-2, frequency matched on age and sex. Among controls, 22 were positive and 22 were negative for one of 27 other respiratory virus pathogens. To assess the impact of COVID-19 on the risk of symptom presence at follow-up (day 30-225 post-enrollment test), we performed log-linear regression with robust standard errors, adjusting for confounding by shelter site and demographic variables determined a priori. RESULTS: Of 53 eligible COVID-19 cases, 22 (42%) completed ≥ 1 follow-up survey. While five (23%) cases reported ≥ 1 symptom at baseline, this increased to 77% (10/13) between day 30-59 and 33% (4/12) day 90 + . The most commonly reported symptoms day 30 + were fatigue (27%) and rhinorrhea (27%), with 8 (36%) reporting symptoms that interfered with or prevented daily activities. Four (33%) symptomatic cases reported receiving medical care outside of a medical provider at an isolation facility. Of 44 controls, 12 (27%) reported any symptoms day 90 + . Risk of any symptoms at follow-up was 5.4 times higher among COVID-19 cases compared to controls (95% CI: 2.7-10.5). CONCLUSIONS: Shelter residents reported a high prevalence of symptoms 30 + days after their SARS-CoV-2 detection, though few accessed medical care for persistent illness. The impact of COVID-19 extends beyond acute illness and may exacerbate existing challenges that marginalized populations face in maintaining their health and wellbeing.

Development of novel composite data quality scores to evaluate facility-level data quality in electronic data in Kenya: a nationwide retrospective cohort study.

BACKGROUND: In this evaluation, we aim to strengthen Routine Health Information Systems (RHIS) through the digitization of data quality assessment (DQA) processes. We leverage electronic data from the Kenya Health Information System (KHIS) which is based on the District Health Information System version 2 (DHIS2) to perform DQAs at scale. We provide a systematic guide to developing composite data quality scores and use these scores to assess data quality in Kenya. METHODS: We evaluated 187 HIV care facilities with electronic medical records across Kenya. Using quarterly, longitudinal KHIS data from January 2011 to June 2018 (total N = 30 quarters), we extracted indicators encompassing general HIV services including services to prevent mother-to-child transmission (PMTCT). We assessed the accuracy (the extent to which data were correct and free of error) of these data using three data-driven composite scores: 1) completeness score; 2) consistency score; and 3) discrepancy score. Completeness refers to the presence of the appropriate amount of data. Consistency refers to uniformity of data across multiple indicators. Discrepancy (measured on a Z-scale) refers to the degree of alignment (or lack thereof) of data with rules that defined the possible valid values for the data. RESULTS: A total of 5,610 unique facility-quarters were extracted from KHIS. The mean completeness score was 61.1% [standard deviation (SD) = 27%]. The mean consistency score was 80% (SD = 16.4%). The mean discrepancy score was 0.07 (SD = 0.22). A strong and positive correlation was identified between the consistency score and discrepancy score (correlation coefficient = 0.77), whereas the correlation of either score with the completeness score was low with a correlation coefficient of -0.12 (with consistency score) and -0.36 (with discrepancy score). General HIV indicators were more complete, but less consistent, and less plausible than PMTCT indicators. CONCLUSION: We observed a lack of correlation between the completeness score and the other two scores. As such, for a holistic DQA, completeness assessment should be paired with the measurement of either consistency or discrepancy to reflect distinct dimensions of data quality. Given the complexity of the discrepancy score, we recommend the simpler consistency score, since they were highly correlated. Routine use of composite scores on KHIS data could enhance efficiencies in DQA at scale as digitization of health information expands and could be applied to other health sectors beyondHIV clinics.

Sample Size Calculations for Stepped Wedge Designs with Treatment Effects that May Change with the Duration of Time under Intervention.

The stepped wedge design is often used to evaluate interventions as they are rolled out across schools, health clinics, communities, or other clusters. Most models used in the design and analysis of stepped wedge trials assume that the intervention effect is immediate and constant over time following implementation of the intervention (the "exposure time"). This is known as the IT (immediate treatment effect) assumption. However, recent research has shown that using methods based on the IT assumption when the treatment effect varies over exposure time can give extremely misleading results. In this manuscript, we discuss the need to carefully specify an appropriate measure of the treatment effect when the IT assumption is violated and we show how a stepped wedge trial can be powered when it is anticipated that the treatment effect will vary as a function of the exposure time. Specifically, we describe how to power a trial when the exposure time indicator (ETI) model of Kenny et al. (Statistics in Medicine, 41, 4311-4339, 2022) is used and the estimand of interest is a weighted average of the time-varying treatment effects. We apply these methods to the ADDRESS-BP trial, a type 3 hybrid implementation study designed to address racial disparities in health care by evaluating a practice-based implementation strategy to reduce hypertension in African American communities.

Improving domestic violence screening practices in the emergency department: an Australian perspective.

INTRODUCTION: Domestic violence (DV) is a major cause of morbidity worldwide. The ED is a location recommended for opportunistic screening. However, screening within EDs remains irregular. OBJECTIVE: To examine intrinsic and extrinsic barriers to routine screening in Australian EDs, while describing actions taken after identification of DV. METHODS: Emergency clinicians at nine public hospitals participated in an anonymous online survey. Factor analysis was performed to identify principal components around attitudes and beliefs towards screening. RESULTS: In total, 496 emergency clinicians participated. Universal screening was uncommon; less than 2% of respondents reported screening all adults or all women. Although willing, nearly half (45%) reported not knowing how to screen. High patient load and no single rooms were 'very or severely limiting' for 88% of respondents, respectively, while 24/7 social work and interpreter services, and online/written DV protocols were top enablers. Factor analysis identified four distinct intrinsic belief components: (1) screening is not futile and could be done in ED, (2) screening will not cause harm, (3) there is a duty to screen and (4) I am willing to screen. CONCLUSION: This study describes a culture of Queensland ED clinicians that believe DV screening in ED is important and interventions are effective. Most ED clinicians are willing to screen. In this setting, availability of social work and interpreter services are important mitigating resources. Clinician education focusing on duty to screen, coupled with a built-in screening tool, and e-links to a local management protocol may improve the uptake of screening and subsequently increase detection.