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.

Genomic epidemiology and evolution of rhinovirus in western Washington State, 2021-22.

BACKGROUND: Human rhinoviruses (RV) primarily cause the common cold, but infection outcomes vary from subclinical to severe cases, including asthma exacerbations and fatal pneumonia in immunocompromised individuals. To date, therapeutic strategies have been hindered by the high diversity of serotypes. Global surveillance efforts have traditionally focused on sequencing VP1 or VP2/VP4 genetic regions, leaving gaps in our understanding of RV genomic diversity. METHODS: We sequenced 1,078 RV genomes from nasal swabs of symptomatic and asymptomatic individuals to explore viral evolution during two epidemiologically distinct periods in Washington State: when the COVID-19 pandemic affected the circulation of other seasonal respiratory viruses except for RV (February - July 2021), and when the seasonal viruses reemerged with the severe RSV and influenza outbreak (November-December 2022). We constructed maximum likelihood and BEAST-phylodynamic trees to characterize intra-genotype evolution. RESULTS: We detected 99 of 168 known genotypes and observed inter-genotypic recombination and genotype cluster swapping from 2021 to 2022. We found a significant association between the presence of symptoms and viral load, but not with RV species or genotype. Phylodynamic trees, polyprotein selection pressure, and Shannon entropy revealed co-circulation of divergent clades within genotypes with high amino acid constraints throughout polyprotein. DISCUSSION: Our study underscores the dynamic nature of RV genomic epidemiology within a localized geographic region, as more than 20% of existing genotypes within each RV species co-circulated each studied month. Our findings also emphasize the importance of investigating correlations between rhinovirus genotypes and serotypes to understand long-term immunity and cross-protection.

Genomic Characterization of Respiratory Syncytial Virus during 2022-23 Outbreak, Washington, USA.

We sequenced 54 respiratory syncytial virus (RSV) genomes collected during 2021-22 and 2022-23 outbreaks in Washington, USA, to determine the origin of increased RSV cases. Detected RSV strains have been spreading for >10 years, suggesting a role for diminished population immunity from low RSV exposure during the COVID-19 pandemic.

Ex Vivo and In Vivo CD46 Receptor Utilization by Species D Human Adenovirus Serotype 26 (HAdV26).

Human adenovirus serotype 26 (Ad26) is used as a gene-based vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and HIV-1. However, its primary receptor portfolio remains controversial, potentially including sialic acid, coxsackie and adenovirus receptor (CAR), integrins, and CD46. We and others have shown that Ad26 can use CD46, but these observations were questioned on the basis of the inability to cocrystallize Ad26 fiber with CD46. Recent work demonstrated that Ad26 binds CD46 with its hexon protein rather than its fiber. We examined the functional consequences of Ad26 for infection in vitro and in vivo. Ectopic expression of human CD46 on Chinese hamster ovary cells increased Ad26 infection significantly. Deletion of the complement control protein domain CCP1 or CCP2 or the serine-threonine-proline (STP) region of CD46 reduced infection. Comparing wild-type and sialic acid-deficient CHO cells, we show that the usage of CD46 is independent of its sialylation status. Ad26 transduction was increased in CD46 transgenic mice after intramuscular (i.m.) injection but not after intranasal (i.n.) administration. Ad26 transduction was 10-fold lower than Ad5 transduction after intratumoral (i.t.) injection of CD46-expressing tumors. Ad26 transduction of liver was 1,000-fold lower than that ofAd5 after intravenous (i.v.) injection. These data demonstrate the use of CD46 by Ad26 in certain situations but also show that the receptor has little consequence by other routes of administration. Finally, i.v. injection of high doses of Ad26 into CD46 mice induced release of liver enzymes into the bloodstream and reduced white blood cell counts but did not induce thrombocytopenia. This suggests that Ad26 virions do not induce direct clotting side effects seen during coronavirus disease 2019 (COVID-19) vaccination with this serotype of adenovirus. IMPORTANCE The human species D Ad26 is being investigated as a low-seroprevalence vector for oncolytic virotherapy and gene-based vaccination against HIV-1 and SARS-CoV-2. However, there is debate in the literature about its tropism and receptor utilization, which directly influence its efficiency for certain applications. This work was aimed at determining which receptor(s) this virus uses for infection and its role in virus biology, vaccine efficacy, and, importantly, vaccine safety.

The Clinical and Genomic Epidemiology of Rhinovirus in Homeless Shelters-King County, Washington.

BACKGROUND: Rhinovirus (RV) is a common cause of respiratory illness in all people, including those experiencing homelessness. RV epidemiology in homeless shelters is unknown. METHODS: We analyzed data from a cross-sectional homeless shelter study in King County, Washington, October 2019-May 2021. Shelter residents or guardians aged ≥3 months reporting acute respiratory illness completed questionnaires and submitted nasal swabs. After 1 April 2020, enrollment expanded to residents and staff regardless of symptoms. Samples were tested by multiplex RT-PCR for respiratory viruses. A subset of RV-positive samples was sequenced. RESULTS: There were 1066 RV-positive samples with RV present every month of the study period. RV was the most common virus before and during the coronavirus disease 2019 (COVID-19) pandemic (43% and 77% of virus-positive samples, respectively). Participants from family shelters had the highest prevalence of RV. Among 131 sequenced samples, 33 RV serotypes were identified with each serotype detected for ≤4 months. CONCLUSIONS: RV infections persisted through community mitigation measures and were most prevalent in shelters housing families. Sequencing showed a diversity of circulating RV serotypes, each detected over short periods of time. Community-based surveillance in congregate settings is important to characterize respiratory viral infections during and after the COVID-19 pandemic. CLINICAL TRIALS REGISTRATION: NCT04141917.

Human Parainfluenza Virus in Homeless Shelters before and during the COVID-19 Pandemic, Washington, USA.

To determine the epidemiology of human parainfluenza virus in homeless shelters during the COVID-19 pandemic, we analyzed data and sequences from respiratory specimens collected in 23 shelters in Washington, USA, during 2019-2021. Two clusters in children were genetically similar by shelter of origin. Shelter-specific interventions are needed to reduce these infections.

Medical and Surgical Management of Hidradenitis Suppurativa: A Review of International Treatment Guidelines and Implementation in General Dermatology Practice.

BACKGROUND: Hidradenitis suppurativa (HS) is a chronic painful skin disease that severely impairs patients' quality of life. While high-quality trials of HS therapies remain limited, medical knowledge of best treatment practices is rapidly evolving, leading to the recent publication of multiple international treatment guidelines for HS. SUMMARY: This review compares international HS treatment guidelines, describes evidence for effectiveness of common and emerging HS therapies, and provides guidance for integrating evidence-based HS care into practice. Although over 50 medical and procedural treatments are mentioned across international HS guidelines, only adalimumab and infliximab have grade B/weak recommendation or higher across all major guidelines. This review describes the appropriate patient selection and effectiveness of the most commonly used medical and procedural treatments for HS. It also includes recommendations for counseling, dosing, and duration of medical therapies as well as procedure videos for the practicing dermatologist.

An open-label study of anakinra for the treatment of moderate to severe hidradenitis suppurativa.

BACKGROUND: Hidradenitis suppurativa (HS) is a chronic inflammatory disorder characterized by sterile abscesses and fistulae predominantly affecting the axillae and groin. Various biologic agents have been attempted for HS, but there is still no definitive treatment. OBJECTIVES: We sought to evaluate the efficacy, safety, and tolerability of anakinra in the treatment of moderate to severe HS. METHODS: Six patients with moderate to severe HS were enrolled in an open-label study with all patients receiving active treatment for 8 weeks with an additional 8 weeks of follow-up off therapy. RESULTS: The 5 patients who completed the 8-week therapy showed a significant mean decrease in their modified Sartorius score of 34.8 points. The physician and patient global assessment of overall activity showed significant reductions between baseline and 8 weeks of therapy: 45.8 points and 35.6 points, respectively. The Dermatology Life Quality Index showed a significant reduction after 8 weeks of treatment with anakinra. Functional T-cell analysis revealed that patients had increased percentages of CD3(+) T cells in lesional skin compared with nonlesional skin before therapy. LIMITATIONS: The limited number of patients and lack of control group are limitations. CONCLUSIONS: Anakinra demonstrated decreased HS disease activity by both objective and subjective measures.

Autoinflammation: From monogenic syndromes to common skin diseases.

Autoinflammation is characterized by aberrant regulation of the innate immune system and often manifests as periodic fevers and systemic inflammation involving multiple organs, including the skin. Mutations leading to abnormal behavior or activity of the interleukin 1 beta (IL-1ß)-processing inflammasome complex have been found in several rare autoinflammatory syndromes, for which anticytokine therapy such as IL-1 or tumor necrosis factor-alfa inhibition may be effective. It is becoming clear that features of autoinflammation also affect common dermatoses, some of which were previously thought to be solely autoimmune in origin (eg, vitiligo, systemic lupus erythematosus). Recognizing the pathogenetic role of autoinflammation can open up new avenues for the targeted treatment of complex, inflammatory dermatoses.

Compassionate care: enhancing physician-patient communication and education in dermatology: Part I: Patient-centered communication.

The motivation for developing patient-centered communication stems from a desire to enhance the quality of patient care, fulfill professional competency requirements, reduce medical errors, and improve health outcomes and patient satisfaction. Patient-centered communication skills can optimize the physician-patient relationship without significantly prolonging office visits. We propose a series of practical and generally effective techniques for verbal and nonverbal communication. We also suggest a targeted approach for specific difficult conversations that may occur frequently in the practice of dermatology.

Compassionate care: enhancing physician-patient communication and education in dermatology: Part II: Patient education.

Patient education is a fundamental part of caring for patients. A practice gap exists, where patients want more information, while health care providers are limited by time constraints or difficulty helping patients understand or remember. To provide patient-centered care, it is important to assess the needs and goals, health beliefs, and health literacy of each patient. This allows health care providers to individualize education for patients. The use of techniques, such as gaining attention, providing clear and memorable explanations, and assessing understanding through "teach-back," can improve patient education. Verbal education during the office visit is considered the criterion standard. However, handouts, visual aids, audiovisual media, and Internet websites are examples of teaching aids that can be used as an adjunct to verbal instruction. Part II of this 2-part series on patient-physician interaction reviews the importance and need for patient education along with specific guidelines and techniques that can be used.

Treatment of psoriasis and long-term maintenance using 308 nm excimer laser, clobetasol spray, and calcitriol ointment: a case series.

Psoriasis is a chronic inflammatory skin disease that is characterized by thickened red plaques covered with silvery scales. Excimer laser therapy is a cutting-edge advancement in UVB phototherapy. In contrast to traditional phototherapy, the 308 nm excimer laser only targets psoriasis plaques, while it spares uninvolved skin. It allows for treatment with a supra-erythmogenic dose of UVB irradiation. Targeted UVB therapy is a possible treatment especially for many who have failed topical treatments, systemic therapy, and traditional phototherapy. For safe and effective psoriasis treatment, a combination of therapies may be used, including a combination of laser treatment with topical medications. We present two cases demonstrating effective treatment with excimer laser in conjunction with clobetasol spray and calcitriol ointment for 12 weeks. Long-term near-clearance of psoriasis was sustained after 6 months and one-year follow up periods without further therapy.

Multiple cutaneous plexiform schwannomas as initial presentation of neurofibromatosis 2 in a 9-year-old.

Neurofibromatosis 2 (NF2) is an autosomal-dominant disease caused by genetic mutations of the NF2 gene on chromosome 22. Patients are often diagnosed according to the presence of bilateral vestibular schwannomas and other tumors in the brain and spinal cord. In children, NF2 can present early with ocular findings and cutaneous tumors. We report here a 9-year-old girl who presented with multiple pigmented, slightly tender plaques on her scalp, face, and back that were revealed by histopathology to be plexiform schwannomas. We suspected NF2 and sent the patient's blood for genetic testing, which confirmed our diagnosis.

Excimer laser therapy for hairline psoriasis: a useful addition to the scalp psoriasis treatment algorithm.

Psoriasis is a chronic, inflammatory skin condition with negative impacts both physical and psychological. Scalp psoriasis, especially around the hairline, can cause significant impairment in quality of life due to its visibility. Options for treatment of facial psoriasis, including hairline involvement, are the use of low potency topical steroids, calcineurin inhibitors, and vitamin D analogues. Though the use of excimer laser for scalp psoriasis has been reported, there are no cases or studies specifically examining excimer laser phototherapy for the treatment of hairline psoriasis. We present a case of rapid improvement of hairline psoriasis using a regimen of 308 nm excimer laser with clobetasol spray and recommend an algorithm for the optimal treatment of scalp psoriasis utilizing currently available antipsoriatic therapies.

In Situ Micro-Observation of Surface Roughness and Fracture Mechanism in Metal Microforming of Thin Copper Sheets with Newly Developed Compact Testing Apparatus.

A better understanding of material deformation behaviours with changes in size is crucial to the design and operation of metal microforming processes. In order to facilitate the investigation of size effects, material deformation behaviours needed to be determined directly from material characterizations. This study was aimed at the design and manufacture of a compact universal testing machine (UTM) compatible with a 3D laser-confocal microscope to observe the deformation behaviour of materials in real-time. In this study, uniaxial micro tensile testing was conducted on three different thin (0.05 mm, 0.1 mm, and 0.3 mm) copper specimens with characteristic dimensions at micro scales. Micro tensile experimental runs were carried out on copper specimens with varying grain sizes on the newly developed apparatus under a 3D laser-confocal microscope. Microscale experiments under 3D laser-confocal microscope provided not only a method to observe the microstructure of materials, but also a novel way to observe the early stages of fracture mechanisms. From real-time examination using the newly developed compact testing apparatus, we discovered that fracture behaviour was mostly brought about by the concave surface formed by free surface roughening. Findings with high stability were discovered while moving with the sample grasped along the drive screw in the graphical plot of a crosshead's displacement against time. Our results also showed very low mechanical noise (detected during the displacement of the crosshead), which indicated that there were no additional effects on the machine, such as vibrations or shifts in speed that could influence performance. The engineering stress-strain plots of the pure copper-tests with various thicknesses or samples depicted a level of stress necessary to initiate plastic flowing inside the material. From these results, we observed that strength and ductility declined with decreasing thickness. The influence of thickness on fracture-strain, observed during tensile testing, made it clear that the elongation-at-break of the pure-copper foils intensely decreased with decreases in thickness. The relative average surface-roughness Ra was evaluated, which showed us that the surface-roughness escalated with the increasing trend of plasticity deformation (plastic strain) ε. For better understanding of the effects of plastic strain on surface roughness prior to material fractures, micro tensile tests were performed on the newly developed machine under a 3D laser-confocal-microscope. We observed that homogeneous surface roughness was caused by plastic strain, which further formed the concave surface that led to the fracture points. Finally, we concluded that surface roughness was one of the crucial factors influencing the fracture behaviour of metallic sheet-strips in metal microforming. We found that this type of testing apparatus could be designed and manufactured within a manageable budget.

The clinical and genomic epidemiology of seasonal human coronaviruses in congregate homeless shelter settings: A repeated cross-sectional study.

Background: The circulation of respiratory viruses poses a significant health risk among those residing in congregate settings. Data are limited on seasonal human coronavirus (HCoV) infections in homeless shelter settings. Methods: We analysed data from a clinical trial and SARS-CoV-2 surveillance study at 23 homeless shelter sites in King County, Washington between October 2019-May 2021. Eligible participants were shelter residents aged ≥3 months with acute respiratory illness. We collected enrolment data and nasal samples for respiratory virus testing using multiplex RT-PCR platform including HCoV. Beginning April 1, 2020, eligibility expanded to shelter residents and staff regardless of symptoms. HCoV species was determined by RT-PCR with species-specific primers, OpenArray assay or genomic sequencing for samples with an OpenArray relative cycle threshold <22. Findings: Of the 14,464 samples from 3281 participants between October 2019-May 2021, 107 were positive for HCoV from 90 participants (median age 40 years, range: 0·9-81 years, 38% female). HCoV-HKU1 was the most common species identified before and after community-wide mitigation. No HCoV-positive samples were identified between May 2020-December 2020. Adults aged ≥50 years had the highest detection of HCoV (11%) among virus-positive samples among all age-groups. Species and sequence data showed diversity between and within HCoV species over the study period. Interpretation: HCoV infections occurred in all congregate homeless shelter site age-groups with the greatest proportion among those aged ≥50 years. Species and sequencing data highlight the complexity of HCoV epidemiology within and between shelters sites. Funding: Gates Ventures, Centers for Disease Control and Prevention, National Institute of Health.

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.

Longitudinal TprK profiling of in vivo and in vitro-propagated Treponema pallidum subsp. pallidum reveals accumulation of antigenic variants in absence of immune pressure.

Immune evasion by Treponema pallidum subspecies pallidum (T. pallidum) has been attributed to antigenic variation of its putative outer-membrane protein TprK. In TprK, amino acid diversity is confined to seven variable (V) regions, and generation of sequence diversity within the V regions occurs via a non-reciprocal segmental gene conversion mechanism where donor cassettes recombine into the tprK expression site. Although previous studies have shown the significant role of immune selection in driving accumulation of TprK variants, the contribution of baseline gene conversion activity to variant diversity is less clear. Here, combining longitudinal tprK deep sequencing of near clonal Chicago C from immunocompetent and immunosuppressed rabbits along with the newly developed in vitro cultivation system for T. pallidum, we directly characterized TprK alleles in the presence and absence of immune selection. Our data confirm significantly greater sequence diversity over time within the V6 region during syphilis infection in immunocompetent rabbits compared to immunosuppressed rabbits, consistent with previous studies on the role of TprK in evasion of the host immune response. Compared to strains grown in immunocompetent rabbits, strains passaged in vitro displayed low level changes in allele frequencies of TprK variable region sequences similar to that of strains passaged in immunosuppressed rabbits. Notably, we found significantly increased rates of V6 allele generation relative to other variable regions in in vitro cultivated T, pallidum strains, illustrating that the diversity within these hypervariable regions occurs in the complete absence of immune selection. Together, our results demonstrate antigenic variation in T. pallidum can be studied in vitro and occurs even in the complete absence of immune pressure, allowing the T. pallidum population to continuously evade the immune system of the infected host.

Adherence to highly active antiretroviral therapy among people living with HIV and associated high-risk behaviours and clinical characteristics: A cross-sectional survey in Vietnam.

Although Vietnam has promoted the utilisation of highly active antiretroviral therapy (HAART) towards HIV elimination targets, adherence to treatment has remained under-investigated. We aimed to describe high-risk behaviours and clinical characteristics by adherence status and to identify the factors associated with non-adherence. We included 426 people living with HIV (PLWH) currently or previously involved in HAART. Most participants were men (75.4%), young (33.6 years), with low income and low education levels. Non-adherent PLWH (11.5%) were more likely to have a larger number of sex partners (p-value = 0.053), sex without condom use (p-value = 0.007) and not receive result at hospital or voluntary test centre (p-value = 0.001). Multiple logistic regression analysis showed that demographic (education levels), sexual risk behaviours (multiple sex partners and sex without using condom) and clinical characteristics (time and facility at first time received HIV-positive result) were associated with HAART non-adherence. There are differences in associated factors between women (education levels and place of HIV testing) and men (multiple sex partners). Gender-specific programs, changing risky behaviours and reducing harms among PLWH may benefit adherence. We highlight the need to improve the quantity and quality of HIV/AIDS services in Vietnam, especially in pre- and post-test counselling, to achieve better HAART adherence, working towards ending AIDS in 2030.