Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county.

SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape.

Cost-utility analysis of a palliative care program in Colombia.

BACKGROUND: The economic assessment of health care models in palliative care promotes their global development. The purpose of the study is to assess the cost-effectiveness of a palliative care program (named Contigo) with that of conventional care from the perspective of a health benefit plan administrator company, Sanitas, in Colombia. METHODS: The incremental cost-utility ratio (ICUR) and the incremental net monetary benefit (INMB) were estimated using micro-costing in a retrospective, analytical cross-sectional study on the care of terminally ill patients enrolled in a palliative care program. A 6-month time horizon prior to death was used. The EQ-5D-3 L questionnaire (EQ-5D-3 L) and the McGill Quality of Life Questionnaire (MQOL) were used to measure the quality of life. RESULTS: The study included 43 patients managed within the program and 16 patients who received conventional medical management. The program was less expensive than the conventional practice (difference of 1,924.35 US dollars (USD), P = 0.18). When compared to the last 15 days, there is a higher perception of quality of life, which yielded 0.25 in the EQ-5D-3 L (p < 0.01) and 1.55 in the MQOL (P < 0.01). The ICUR was negative and the INMB was positive. CONCLUSION: Because the Contigo program reduces costs while improving quality of life, it is considered to be net cost-saving and a model with value in health care. Greater availability of palliative care programs, such as Contigo, in Colombia can help reduce existing gaps in access to universal palliative care health coverage, resulting in more cost-effective care.

Associations Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants and Risk of Coronavirus Disease 2019 (COVID-19) Hospitalization Among Confirmed Cases in Washington State: A Retrospective Cohort Study.

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with 7 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. METHODS: Our study includes individuals with positive SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) in the Washington Disease Reporting System with available viral genome data, from 1 December 2020 to 14 January 2022. The analysis was restricted to cases with specimens collected through sentinel surveillance. Using a Cox proportional hazards model with mixed effects, we estimated hazard ratios (HR) for hospitalization risk following infection with a variant, adjusting for age, sex, calendar week, and vaccination. RESULTS: In total, 58 848 cases were sequenced through sentinel surveillance, of which 1705 (2.9%) were hospitalized due to COVID-19. Higher hospitalization risk was found for infections with Gamma (HR 3.20, 95% confidence interval [CI] 2.40-4.26), Beta (HR 2.85, 95% CI 1.56-5.23), Delta (HR 2.28 95% CI 1.56-3.34), or Alpha (HR 1.64, 95% CI 1.29-2.07) compared to infections with ancestral lineages; Omicron (HR 0.92, 95% CI .56-1.52) showed no significant difference in risk. Following Alpha, Gamma, or Delta infection, unvaccinated patients show higher hospitalization risk, while vaccinated patients show no significant difference in risk, both compared to unvaccinated, ancestral lineage cases. Hospitalization risk following Omicron infection is lower with vaccination. CONCLUSIONS: Infection with Alpha, Gamma, or Delta results in a higher hospitalization risk, with vaccination attenuating that risk. Our findings support hospital preparedness, vaccination, and genomic surveillance.

Effectiveness of the ICCMS caries management system for children: a 3-year multicentre randomised controlled trial.

OBJECTIVE: This 3-year multicentre randomised controlled trial compared, in 6-7-year-old Colombian children, the effectiveness of the ICCMS (International Caries Classification and Management System) with a conventional caries-management system (CCMS) in terms of individual caries-risk, caries lesions, and secondarily, oral-health-related knowledge/attitudes/practices, and number of appointments. MATERIAL AND METHODS: With ethical approval, 240 6-7-year olds from six Colombian clinics were recruited. Trained examiners conducted the following baseline/follow-up assessments: Caries risk (Cariogram-ICCMS); caries severity/activity staging (ICDAS-merged combined radiographic/visual); sealants/fillings/missing teeth, and oral-health-related knowledge, attitudes and practices. Children received their randomly allocated (ICCMS/CCMS) care from dental practitioners. Outcomes: caries-risk control (children); caries-progression control (tooth surfaces); oral-health-related knowledge/attitudes/practices improvement (parents/children), and appointments' number (children). Descriptive and non-parametric/parametric bivariate analyses were performed. RESULTS: Three-year-follow-up: n = 187 (77.9%; ICCMS: n = 92; CCMS: n = 95) disclosed a baseline-to-3-year overall high-caries-risk children decrease (ICCMS: 60.9-0%, p < .001; CCMS: 54.7-5.3%, p < .001) (p > .05). ICCMS versus CCMS showed: fewer tooth-surface caries progression (6.2% vs 7.1%, p = .010) and fewer active-caries lesions (49.8% vs. 59.1%, p < .05); higher proportion of children with ≥2/day fluoride-toothpaste tooth-brushing practice (p < .05); similar mean number of appointments (10.9 ± 5.9 vs. 10.0 ± 3.8, p = .15). CONCLUSION: Both caries-management systems showed similar effectiveness in caries-risk control, with ICCMS more effectively controlling tooth-surface caries progression and improving toothbrushing practices.

SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing.

BACKGROUND: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse-transcription PCR (RT-qPCR). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce. To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS: We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS: After optimization, SwabExpress has a low limit of detection at 2-4 molecules/µL, 100% sensitivity, and 99.4% specificity when compared side by side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION: SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.

CariesCare International adapted for the pandemic in children: Caries OUT multicentre single-group interventional study protocol.

BACKGROUND: Comprehensive caries care has shown effectiveness in controlling caries progression and improving health outcomes by controlling caries risk, preventing initial-caries lesions progression, and patient satisfaction. To date, the caries-progression control effectiveness of the patient-centred risk-based CariesCare International (CCI) system, derived from ICCMS™ for the practice (2019), remains unproven. With the onset of the COVID-19 pandemic a previously planned multi-centre RCT shifted to this "Caries OUT" study, aiming to assess in a single-intervention group in children, the caries-control effectiveness of CCI adapted for the pandemic with non-aerosols generating procedures (non-AGP) and reducing in-office time. METHODS: In this 1-year multi-centre single-group interventional trial the adapted-CCI effectiveness will be assessed in one single group in terms of tooth-surface level caries progression control, and secondarily, individual-level caries progression control, children's oral-health behaviour change, parents' and dentists' process acceptability, and costs exploration. A sample size of 258 3-5 and 6-8 years old patients was calculated after removing half from the previous RCT, allowing for a 25% dropout, including generally health children (27 per centre). The single-group intervention will be the adapted-CCI 4D-cycle caries care, with non-AGP and reduced in-office appointments' time. A trained examiner per centre will conduct examinations at baseline, at 5-5.5 months (3 months after basic management), 8.5 and 12 months, assessing the child's CCI caries risk and oral-health behaviour, visually staging and assessing caries-lesions severity and activity without air-drying (ICDAS-merged Epi); fillings/sealants; missing/dental-sepsis teeth, and tooth symptoms, synthetizing together with parent and external-trained dental practitioner (DP) the patient- and tooth-surface level diagnoses and personalised care plan. DP will deliver the adapted-CCI caries care. Parents' and dentists' process acceptability will be assessed via Treatment-Evaluation-Inventory questionnaires, and costs in terms of number of appointments and activities. Twenty-one centres in 13 countries will participate. DISCUSSION: The results of Caries OUT adapted for the pandemic will provide clinical data that could help support shifting the caries care in children towards individualised oral-health behaviour improvement and tooth-preserving care, improving health outcomes, and explore if the caries progression can be controlled during the pandemic by conducting non-AGP and reducing in-office time. TRIAL REGISTRATION: Retrospectively-registered-ClinicalTrials.gov-NCT04666597-07/12/2020: https://register.clinicaltrials.gov/prs/app/action/SelectProtocol?sid=S000AGM4&selectaction=Edit&uid=U00019IE&ts=2&cx=uwje3h . Protocol-version 2: 27/01/2021.

Caries status in young Colombian children expressed by the ICCMS™ visual/radiographic combined caries staging system.

OBJECTIVE: To report (1) the caries experience prevalence and mean, and the caries severity and distribution patterns, expressed clinically and combined with radiographs with the conventional and ICCMS™ systems in young children from Bogotá, Colombia; (2) the contribution of including radiographs to the clinical caries scoring and (3) in which surfaces the radiograph adds to the clinical caries registration. MATERIAL AND METHODS: Six hundred children from kindergartens/schools were enrolled: Cohort A: 2-year (n = 200), Cohort B: 4-year (n = 200) and Cohort C: 6-year (n = 200) olds. Radiographs were taken of the 4- and 6- year olds. Children were examined clinically using the Clinical (C) and Radiographic (R) ICCMS™-epi Caries Scoring Systems, staging caries lesions (d) as: Initial (Cepi/RA), Moderate (CM/RB) or Extensive (CE/RC). Caries experience including missing (m) and filled (f) surfaces was expressed as follows: clinical conventional (CdMEmfs); clinical ICCMS™ (CdepiMEmfs); combined conventional (C + RdMEmfs) and combined ICCMS™ (C + RdepiMEmfs). RESULTS: The prevalence of CdMEmfs was: Cohort A: 32%; Cohort B: 59%; Cohort C: 67.5%, increasing to 73.5%, 99.8% and 100%, respectively, with the C + R depiMEmfs. The CdMEmfs means doubled when initial caries lesions (Cdepi) and radiographs (R) were included. The d component corresponded to over two-thirds of the caries experience. Findings on the radiographs significantly raised caries experience prevalence and means (p < .02), detecting primarily approximal lesions. Surfaces with highest caries frequency were occlusal/approximal of molar teeth and buccal of upper incisor teeth. CONCLUSION: Participants' caries experience was high. The radiographic assessment significantly contributed to caries experience. Molar and upper incisor teeth were most prone to caries.

Child malnutrition and prenatal care: evidence from three Latin American countries.

OBJECTIVE: To examine the effect of prenatal care (PNC) on the level and distribution of child stunting in three Andean countries-Bolivia, Colombia, and Peru-where expanding access to such care has been an explicit policy intervention to tackle child malnutrition in utero and during early childhood. METHODS: An econometric analysis of cross-sectional Demographic and Health Survey (DHS) data was conducted. The analysis included ordinary least-squares (OLS) regressions, estimates of concentration curves, and decompositions of a concentration index. RESULTS: The analysis shows that the use of PNC in Bolivia, Colombia, and Peru is only weakly associated with a reduction in the level of child malnutrition. CONCLUSIONS: Further expansion of PNC programs is unlikely to play a large role in reducing inequalities in malnutrition.

Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences.

Pathogen genomics can provide insights into disease transmission patterns, but new methods are needed to handle modern large-scale pathogen genome datasets. Genetically proximal viruses indicate epidemiological linkage and are informative about transmission events. Here, we leverage pairs of identical sequences using 114,298 SARS-CoV-2 genomes collected via sentinel surveillance from March 2021 to December 2022 in Washington State, USA, with linked age and residence information to characterize fine-scale transmission. The location of pairs of identical sequences is highly consistent with expectations from mobility and social contact data. Outliers in the relationship between genetic and mobility data can be explained by SARS-CoV-2 transmission between postal codes with male prisons, consistent with transmission between prison facilities. Transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. This work improves our ability to characterize transmission from large pathogen genome datasets.

Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years.

Many studies have used mobile device location data to model SARS-CoV-2 dynamics, yet relationships between mobility behavior and endemic respiratory pathogens are less understood. We studied the effects of population mobility on the transmission of 17 endemic viruses and SARS-CoV-2 in Seattle over a 4-year period, 2018-2022. Before 2020, visits to schools and daycares, within-city mixing, and visitor inflow preceded or coincided with seasonal outbreaks of endemic viruses. Pathogen circulation dropped substantially after the initiation of COVID-19 stay-at-home orders in March 2020. During this period, mobility was a positive, leading indicator of transmission of all endemic viruses and lagging and negatively correlated with SARS-CoV-2 activity. Mobility was briefly predictive of SARS-CoV-2 transmission when restrictions relaxed but associations weakened in subsequent waves. The rebound of endemic viruses was heterogeneously timed but exhibited stronger, longer-lasting relationships with mobility than SARS-CoV-2. Overall, mobility is most predictive of respiratory virus transmission during periods of dramatic behavioral change and at the beginning of epidemic waves.

Bacterial incidence and drug resistance from pathogens recovered from blood, cerebrospinal and pleural fluids in 2019-2020. Results of the Invifar network.

Background: Antimicrobial resistance is a global concern. Analysis of sterile fluids is essential because microorganisms are defined as significant in most cases. Blood, cerebrospinal, and pleural fluids are frequently received in the microbiology lab because they are associated with considerable rates of morbi-mortality. Knowledge of epidemiology in these samples is needed to choose proper empirical treatments due to the importance of reducing selection pressure. Methods: We used retrospective laboratory data of blood, CSF, and pleural fluid collected from patients in Mexico between 2019 and 2020. Each laboratory identified the strains and tested susceptibility using its routine methods. For Streptococcus pneumoniae, a comparative analysis was performed with data from the broth microdilution method. Results: Forty-five centers participated in the study, with 30,746 clinical isolates from blood, 2,429 from pleural fluid, and 2,275 from CSF. For blood and CSF, Staphylococcus epidermidis was the most frequent. For blood, among gram negatives, the most frequent was Escherichia coli. Among Enterobacterales, 9.8% of K. pneumoniae were carbapenem-resistant. For S. pneumoniae, similar resistance percentages were observed for levofloxacin, cefotaxime, and vancomycin. For CSF, the most frequent gram-negative was E. coli. In Acinetobacter baumannii, carbapenem resistance was 71.4%. The most frequent species detected for pleural fluid was E. coli; in A. baumannii, carbapenem resistance was 96.3%. Conclusion: Gram-negative bacteria, with E. coli most prevalent, are frequently recovered from CSF, blood, and pleural fluid. In S. pneumoniae, the routine, conventional methods showed good agreement in detecting resistance percentages for erythromycin, levofloxacin, and vancomycin.

Peripheral neuropathy in leprosy: Clinical manifestations and disability in a Colombian national referral center.

To aim of the paper was to describe the neurological features of the physical examination in patients with Hansen's disease who were treated in Bogotá, Colombia. We carried out a descriptive study of all patients with a Hansen's disease diagnosis treated at a referral center between 2003-2018. There were 327 eligible electronic health records (EHRs) with a final sample of 282 subjects. Leprosy was most common in males (57.45%), median age at the diagnosis was 54 years, and lesions of the lower limbs were more common (75.1%). The median time from disease onset to consult was 12 months. Most of them were classified as having lepromatous leprosy (39.7%). Pain over the median nerve trunk was the most common manifestation of disease (28%), followed by pain over the radial trunk (22%). Sensitive alterations were more common than motor ones. Specifically, the posterior tibial nerve was affected in nearly half of subjects. Dual impairment was more common in the ulnar nerve (13.8%). Some disability was apparent in 23.8% of subjects; predominantly grade 1 disability. Findings regarding age, leprosy type, and the frequency of individual nerve compromise were consistent with reports from other countries. Nerve trunk thickening was infrequent, which might be a consequence of subjectiveness in the examination and sample differences in sex distribution, degree of disability and time since disease onset. The frequency of morbidity and disability found in this sample, though low when compared with other series, fails to meet public health goals, including those limiting disability in younger subjects.

Real-life Effectiveness of Omalizumab in Patients with Severe Allergic Asthma: RELIEF Study.

Introduction: Patients with severe allergic asthma (SAA) are at risk of severe exacerbations. Omalizumab is recommended as an add-on treatment for patients with uncontrolled SAA, despite high-dose inhaled corticosteroids and long acting ß2-agonist combination therapy (standard therapy).RELIEF was a prospective, open label, multicenter study conducted to assess the real-life effectiveness of omalizumab co-administered with standard therapy in patients with SAA for 24 months. Methods: A total of 347 patients aged ≥ 6 years with SAA were enrolled, 285 of whom (8 pediatrics and 277 adolescents and adults) completed this 24-month study. Compared with the 12 months prior to baseline, the mean number of exacerbations was reduced in the overall population at any time interval during the study. Proportion of patients with no exacerbations increased to 77.7% at 24 months from 32.6% at 12 months prior to baseline. A reduction in healthcare resource utilization was also observed. The mean number of specialist visits reduced from baseline (5.8 visits) to 2.4 visits at Month 24. Results: The mean asthma control test score was >19 at every time-point during the study. The rate of Global Evaluation of Treatment Effectiveness (GETE) for asthma response significantly increased at Months 18 and 24 (P <0.05) compared to baseline. Pulmonary function remained relatively stable for the overall study population. There were no new or unexpected safety findings in the study. Conclusion: RELIEF study showed that add-on therapy with omalizumab is effective in reducing exacerbations, healthcare utilization, and improving GETE score in patients with SAA uncontrolled by standard therapy.

Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data.

Background: Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates. Methods: We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel. Results: 21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33·5%), Streptococcus pneumoniae (SPn, 29·0%), SARS-CoV-2 (13.8%) and influenza A/H1N1 (9·6%). 140 potential pathogen pairs were included for analysis, and 56 (40%) pairs yielded significant Ct differences (p < 0.01) between monoinfected and co-infected samples. We observed no virus-virus pairs showing evidence of significant facilitating interactions, and found significant viral load decrease among 37 of 108 (34%) assessed pairs. Samples positive with SPn and a virus were consistently associated with increased SPn load. Conclusions: Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral-SPn facilitation and several examples of viral-viral interference. Multipathogen surveillance is a cost-efficient data collection approach, with added clinical and epidemiological informational value over single-pathogen testing, but requires careful analysis to mitigate selection bias.

Trends in Risk Factors and Symptoms Associated With SARS-CoV-2 and Rhinovirus Test Positivity in King County, Washington, June 2020 to July 2022.

Importance: Few US studies have reexamined risk factors for SARS-CoV-2 positivity in the context of widespread vaccination and new variants or considered risk factors for cocirculating endemic viruses, such as rhinovirus. Objectives: To evaluate how risk factors and symptoms associated with SARS-CoV-2 test positivity changed over the course of the pandemic and to compare these with the risk factors associated with rhinovirus test positivity. Design, Setting, and Participants: This case-control study used a test-negative design with multivariable logistic regression to assess associations between SARS-CoV-2 and rhinovirus test positivity and self-reported demographic and symptom variables over a 25-month period. The study was conducted among symptomatic individuals of all ages enrolled in a cross-sectional community surveillance study in King County, Washington, from June 2020 to July 2022. Exposures: Self-reported data for 15 demographic and health behavior variables and 16 symptoms. Main Outcomes and Measures: Reverse transcription-polymerase chain reaction-confirmed SARS-CoV-2 or rhinovirus infection. Results: Analyses included data from 23 498 individuals. The median (IQR) age of participants was 34.33 (22.42-45.08) years, 13 878 (59.06%) were female, 4018 (17.10%) identified as Asian, 654 (2.78%) identified as Black, and 2193 (9.33%) identified as Hispanic. Close contact with an individual with SARS-CoV-2 (adjusted odds ratio [aOR], 3.89; 95% CI, 3.34-4.57) and loss of smell or taste (aOR, 3.49; 95% CI, 2.77-4.41) were the variables most associated with SARS-CoV-2 test positivity, but both attenuated during the Omicron period. Contact with a vaccinated individual with SARS-CoV-2 (aOR, 2.03; 95% CI, 1.56-2.79) was associated with lower odds of testing positive than contact with an unvaccinated individual with SARS-CoV-2 (aOR, 4.04; 95% CI, 2.39-7.23). Sore throat was associated with Omicron infection (aOR, 2.27; 95% CI, 1.68-3.20) but not Delta infection. Vaccine effectiveness for participants fully vaccinated with a booster dose was 93% (95% CI, 73%-100%) for Delta, but not significant for Omicron. Variables associated with rhinovirus test positivity included being younger than 12 years (aOR, 3.92; 95% CI, 3.42-4.51) and experiencing a runny or stuffy nose (aOR, 4.58; 95% CI, 4.07-5.21). Black race, residing in south King County, and households with 5 or more people were significantly associated with both SARS-CoV-2 and rhinovirus test positivity. Conclusions and Relevance: In this case-control study of 23 498 symptomatic individuals, estimated risk factors and symptoms associated with SARS-CoV-2 infection changed over time. There was a shift in reported symptoms between the Delta and Omicron variants as well as reductions in the protection provided by vaccines. Racial and sociodemographic disparities persisted in the third year of SARS-CoV-2 circulation and were also present in rhinovirus infection. Trends in testing behavior and availability may influence these results.

Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus.

Novel variants continue to emerge in the SARS-CoV-2 pandemic. University testing programs may provide timely epidemiologic and genomic surveillance data to inform public health responses. We conducted testing from September 2021 to February 2022 in a university population under vaccination and indoor mask mandates. A total of 3,048 of 24,393 individuals tested positive for SARS-CoV-2 by RT-PCR; whole genome sequencing identified 209 Delta and 1,730 Omicron genomes of the 1,939 total sequenced. Compared to Delta, Omicron had a shorter median serial interval between genetically identical, symptomatic infections within households (2 versus 6 days, P = 0.021). Omicron also demonstrated a greater peak reproductive number (2.4 versus 1.8), and a 1.07 (95% confidence interval: 0.58, 1.57; P < 0.0001) higher mean cycle threshold value. Despite near universal vaccination and stringent mitigation measures, Omicron rapidly displaced the Delta variant to become the predominant viral strain and led to a surge in cases in a university population.

Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county.

SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape.

Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study.

BACKGROUND: The COVID-19 pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with seven SARS-CoV-2 variants. METHODS: Our study includes individuals with positive SARS-CoV-2 RT-PCR in the Washington Disease Reporting System with available viral genome data, from December 1, 2020 to January 14, 2022. The analysis was restricted to cases with specimens collected through sentinel surveillance. Using a Cox proportional hazards model with mixed effects, we estimated hazard ratios (HR) for hospitalization risk following infection with a variant, adjusting for age, sex, calendar week, and vaccination. FINDINGS: 58,848 cases were sequenced through sentinel surveillance, of which 1705 (2.9%) were hospitalized due to COVID-19. Higher hospitalization risk was found for infections with Gamma (HR 3.20, 95%CI 2.40-4.26), Beta (HR 2.85, 95%CI 1.56-5.23), Delta (HR 2.28 95%CI 1.56-3.34) or Alpha (HR 1.64, 95%CI 1.29-2.07) compared to infections with ancestral lineages; Omicron (HR 0.92, 95%CI 0.56-1.52) showed no significant difference in risk. Following Alpha, Gamma, or Delta infection, unvaccinated patients show higher hospitalization risk, while vaccinated patients show no significant difference in risk, both compared to unvaccinated, ancestral lineage cases. Hospitalization risk following Omicron infection is lower with vaccination. CONCLUSION: Infection with Alpha, Gamma, or Delta results in a higher hospitalization risk, with vaccination attenuating that risk. Our findings support hospital preparedness, vaccination, and genomic surveillance. SUMMARY: Hospitalization risk following infection with SARS-CoV-2 variant remains unclear. We find a higher hospitalization risk in cases infected with Alpha, Beta, Gamma, and Delta, but not Omicron, with vaccination lowering risk. Our findings support hospital preparedness, vaccination, and genomic surveillance.

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing.

BACKGROUND: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS: We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral activation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS: After optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION: SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.

Evaluation of density, volume, height and rate of bone resorption of substitutes of autologous bone grafts for the repair of alveolar clefts in humans: A systematic review.

OBJECTIVE: To assess clinical studies that compare synthetic or enriched natural materials to autologous osseous grafts among individuals with cleft lip and palate to determine which would be the substitute to autologous bone graft for alveolar cleft repair in humans. MATERIALS AND METHODS: Randomized and controlled clinical trials on alveolar clefts treated with synthetic bone substitutes and autogenous bone grafts combined with osteoinductive factors compared with autogenous bone grafts alone (with ≥4-month follow-up and reporting clinical/radiographic data) were considered eligible. MEDLINE, EMBASE, and Central databases were searched for articles published until February 2020. RESULTS: Of 73 eligible articles, 15 were included. Some inductive factors along with iliac crest bone decreased bone reabsorption, preserved the generated bone height/width, and reduced the required autologous bone graft volume. Bone morphogenetic protein (BMP2) as an autologous bone graft substitute, demonstrated satisfactory alveolar defect healing, by avoiding autograft use. Many materials did not yield better outcomes than did autologous grafts; however, hydroxyapatite and collagen complex, hydroxyapatite agarose composite gel, acellular dermal matrix film, fibrin glue, platelet-rich plasma, and deproteinized bovine bone showed similar bone healing outcomes, being an alternative alveolar defect treatment. CONCLUSIONS: BMP2, as an osteoinductive factor along with a synthetic matrix, yields satisfactory bone healing and avoids the need for autologous bone grafts. However, high-quality RCTs are necessary to determine the most effective and safe concentration and protocol of BMP2 utilization as a substitute for the autologous iliac crest bone grafting.