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.

Antibodies to Influenza A(H5N1) Virus in Hunting Dogs Retrieving Wild Fowl, Washington, USA.

We detected antibodies to H5 and N1 subtype influenza A viruses in 4/194 (2%) dogs from Washington, USA, that hunted or engaged in hunt tests and training with wild birds. Historical data provided by dog owners showed seropositive dogs had high levels of exposure to waterfowl.

Lessons Learned from Public Health and State Prison Collaborations during COVID-19 Pandemic and Multifacility Tuberculosis Outbreak, Washington, USA.

The large COVID-19 outbreaks in prisons in the Washington (USA) State Department of Corrections (WADOC) system during 2020 highlighted the need for a new public health approach to prevent and control COVID-19 transmission in the system's 12 facilities. WADOC and the Washington State Department of Health (WADOH) responded by strengthening partnerships through dedicated corrections-focused public health staff, improving cross-agency outbreak response coordination, implementing and developing corrections-specific public health guidance, and establishing collaborative data systems. The preexisting partnerships and trust between WADOC and WADOH, strengthened during the COVID-19 response, laid the foundation for a collaborative response during late 2021 to the largest tuberculosis outbreak in Washington State in the past 20 years. We describe challenges of a multiagency collaboration during 2 outbreak responses, as well as approaches to address those challenges, and share lessons learned for future communicable disease outbreak responses in correctional settings.

Clinical and Genomic Epidemiology of Coxsackievirus A21 and Enterovirus D68 in Homeless Shelters, King County, Washington, USA, 2019-2021.

Congregate homeless shelters are disproportionately affected by infectious disease outbreaks. We describe enterovirus epidemiology across 23 adult and family shelters in King County, Washington, USA, during October 2019-May 2021, by using repeated cross-sectional respiratory illness and environmental surveillance and viral genome sequencing. Among 3,281 participants >3 months of age, we identified coxsackievirus A21 (CVA21) in 39 adult residents (3.0% [95% CI 1.9%-4.8%] detection) across 7 shelters during October 2019-February 2020. We identified enterovirus D68 (EV-D68) in 5 adult residents in 2 shelters during October-November 2019. Of 812 environmental samples, 1 was EV-D68-positive and 5 were CVA21-positive. Other enteroviruses detected among residents, but not in environmental samples, included coxsackievirus A6/A4 in 3 children. No enteroviruses were detected during April 2020-May 2021. Phylogenetically clustered CVA21 and EV-D68 cases occurred in some shelters. Some shelters also hosted multiple CVA21 lineages.

Remembering Jan Amesz (1934-2001): a great gentleman, a major discoverer, and an internationally renowned biophysicist of both oxygenic and anoxygenic photosynthesisa.

We present here the research contributions of Jan Amesz (1934-2001) on deciphering the details of the early physico-chemical steps in oxygenic photosynthesis in plants, algae and cyanobacteria, as well as in anoxygenic photosynthesis in purple, green, and heliobacteria. His research included light absorption and the mechanism of excitation energy transfer, primary photochemistry, and electron transfer steps until the reduction of pyridine nucleotides. Among his many discoveries, we emphasize his 1961 proof, with L. N. M. Duysens, of the "series scheme" of oxygenic photosynthesis, through antagonistic effects of Light I and II on the redox state of cytochrome f. Further, we highlight the following research on oxygenic photosynthesis: the experimental direct proof that plastoquinone and plastocyanin function at their respective places in the Z-scheme. In addition, Amesz's major contributions were in unraveling the mechanism of excitation energy transfer and electron transport steps in anoxygenic photosynthetic bacteria (purple, green and heliobacteria). Before we present his research, focusing on his key discoveries, we provide a glimpse of his personal life. We end this Tribute with reminiscences from three of his former doctoral students (Sigi Neerken; Hjalmar Pernentier, and Frank Kleinherenbrink) and from several scientists (Suleyman Allakhverdiev; Robert Blankenship; Richard Cogdell) including two of the authors (G. Garab and A. Stirbet) of this Tribute.

Socioeconomic gradient in functional difficulties by domain among youth: evidence from Egypt.

This study aims to measure inequalities in the distribution of functional difficulties and their different domains among youth aged 15-29 years in Egypt, according to selected socioeconomic characteristics (e.g. wealth quantiles and education level of the head of the household). The data come from the nationally representative survey, 'Household Observatory Survey', with 10,405 persons aged 15-29 years representing the study sample population. The survey identifies individuals with disabilities using the Washington Group Short questions. Inequalities in disability distribution have been measured by the concentration index (CI). The results indicate that functional difficulties have been concentrated among the poorest youth and households headed by illiterate persons. Rural areas have the highest concentration of disabilities among youth, with the lowest wealth and the lowest educational level of the head of the household. The CI suggests the existence of socioeconomic inequalities in all functional difficulties except for seeing difficulties. Understanding which factors more substantially contribute to inequalities is critical for advancing policies devoted to enhancing the quality of life for individuals with disabilities.

Nematode genome announcement: A chromosome-scale genome assembly for the Pristionchus pacificus reference mapping strain PS1843.

Pristionchus pacificus is a free-living nematode that shares many features with Caenorhabditis elegans, such as its short generation time and hermaphroditism, but also exhibits novel traits, i.e., a mouth-form dimorphism that enables predation. The availability of various genetic tools and genomic resources make it a powerful model organism for comparative studies. Here, we present an updated genome of the P. pacificus strain PS1843 (Washington) that is most widely used for genetic analysis. Assembly of PacBio reads together with reference-guided scaffolding resulted in a chromosome-scale genome spanning 171Mb for the PS1843 strain. Whole genome alignments between the P. pacificus PS1843 genome and the genome of the P. pacificus reference strain PS312 (California) revealed megabase-sized regions on chromosomes III, IV, and X that explain the majority of genome size difference between both strains. The improved PS1843 genome will be useful for future forward genetic studies and evolutionary genomic comparisons at the intra-species level.

Commodification and healthcare in the third sector in England: from gift to commodity-and back?

IMPACT: This article suggests why a different approach may be required for commissioning services from third sector providers than from, say, corporate or public providers. English systems for commissioning third sector providers contain both commodified elements (for example formal procurement, provider competition, commissioner-provider separation) and collaborative, relational elements (for example long-term collaboration, reliance on inter-organizational networks). When the two elements conflicted, commissioners and third sector organizations tended to try to work around the commodified elements in order to preserve and develop the collaborative aspects, which suggests that, in practice, they find de-commodified, collaborative methods better adapted to the commissioning of third sector organizations. ABSTRACT: When publicly-funded services are outsourced, governments still use multiple governance structures to retain some control over the services provided. Using realist methods the authors systematically compared this aspect of community health activities provided by third sector organizations in six English localities during 2020-2022. Two modes of commissioning coexisted. Commodified commissioning largely embodied Washington consensus models of formal, competitive procurement. A contrasting, collaborative mode of commissioning relied more upon relational, long-term co-operation and networking among organizations. When the two modes conflicted, commissioners often favoured the collaborative mode and sought to adjust their commissioning to make it less commodified.

Genomic Analysis of Early Monkeypox Virus Outbreak Strains, Washington, USA.

We conducted a genomic analysis of monkeypox virus sequences collected early in the 2022 outbreak, during July-August , in Washington, USA. Using 109 viral genomes, we found low overall genetic diversity, multiple introductions into the state, ongoing community transmission, and potential for co-infections by multiple strains.

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.

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.

Baylisascaris procyonis Roundworm Infection in Child with Autism Spectrum Disorder, Washington, USA, 2022.

We describe a case of Baylisascaris procyonis roundworm infection in a child in Washington, USA, with autism spectrum disorder. Environmental assessment confirmed nearby raccoon habitation and B. procyonis eggs. B. procyonis infections should be considered a potential cause of human eosinophilic meningitis, particularly among young children and persons with developmental delays.

Using Geospatial Data and Random Forest To Predict PFAS Contamination in Fish Tissue in the Columbia River Basin, United States.

Decision makers in the Columbia River Basin (CRB) are currently challenged with identifying and characterizing the extent of per- and polyfluoroalkyl substances (PFAS) contamination and human exposure to PFAS. This work aims to develop and pilot a methodology to help decision makers target and prioritize sampling investigations and identify contaminated natural resources. Here we use random forest models to predict ∑PFAS in fish tissue; understanding PFAS levels in fish is particularly important in the CRB because fish can be a major component of tribal and indigenous people diet. Geospatial data, including land cover and distances to known or potential PFAS sources and industries, were leveraged as predictors for modeling. Models were developed and evaluated for Washington state and Oregon using limited available empirical data. Mapped predictions show several areas where detectable concentrations of PFAS in fish tissue are predicted to occur, but prior sampling has not yet confirmed. Variable importance is analyzed to identify potentially important sources of PFAS in fish in this region. The cost-effective methodologies demonstrated here can help address sparsity of existing PFAS occurrence data in environmental media in this and other regions while also giving insights into potentially important drivers and sources of PFAS in fish.

An investigation of the seasonal relationships between meteorological factors, water quality, and sporadic cases of Legionnaires' disease in Washington, DC.

Since the discovery of Legionnaires' disease (LD), limited progress has been made in understanding the epidemiology of sporadic cases of LD. Outbreaks have confirmed that air conditioning and potable water systems can be sources of community-acquired LD. However, studying the association between water quality and LD incidence has been challenging due to the heterogeneity of water systems across large geographic areas. Furthermore, although seasonal trends in incidence have been linked to increased rainfall and temperatures, the large geographic units have posed similar difficulties. To address this issue, a retrospective ecological study was conducted in Washington, DC, from 2001 to 2019. The study identified aseasonal pattern of LD incidence, with the majority of cases occurring between June and December, peaking in August, October, and November. Increased temperature was found to be associated with LD incidence. In surface water, higher concentrations of manganese, iron, and strontium were positively associated with LD, while aluminum and orthophosphate showed a negative association. Intreatment plant water, higher concentrations of total organic carbon, aluminum, barium, and chlorine were positively associated with LD, while strontium, zinc, and orthophosphate showed a negative association. The results for orthophosphates and turbidity were inconclusive, indicating the need for further research.

Association between any underlying health condition and COVID-19-associated hospitalization by age group, Washington State, 2020-2021: a retrospective cohort study.

BACKGROUND: Presence of at least one underlying health condition (UHC) is positively associated with severe COVID-19, but there is limited research examining this association by age group, particularly among young adults. METHODS: We examined age-stratified associations between any UHC and COVID-19-associated hospitalization using a retrospective cohort study of electronic health record data from the University of Washington Medicine healthcare system for adult patients with a positive SARS-CoV-2 test from February 29, 2020, to March 13, 2021. Any UHC was defined as documented diagnosis of at least one UHC identified by the CDC as a potential risk factor for severe COVID-19. Adjusting for sex, age, race and ethnicity, and health insurance, we estimated risk ratios (aRRs) and risk differences (aRDs), overall and by age group (18-39, 40-64, and 65 + years). RESULTS: Among patients aged 18-39 (N = 3,249), 40-64 (N = 2,840), 65 + years (N = 1,363), and overall (N = 7,452), 57.5%, 79.4%, 89.4%, and 71.7% had at least one UHC, respectively. Overall, 4.4% of patients experienced COVID-19-associated hospitalization. For all age groups, the risk of COVID-19-associated hospitalization was greater for patients with any UHC vs. those without (18-39: 2.2% vs. 0.4%; 40-64: 5.6% vs. 0.3%; 65 + : 12.2% vs. 2.8%; overall: 5.9% vs. 0.6%). The aRR comparing patients with vs. those without UHCs was notably higher for patients aged 40-64 years (aRR [95% CI] for 18-39: 4.3 [1.8, 10.0]; 40-64: 12.9 [3.2, 52.5]; 65 + : 3.1 [1.2, 8.2]; overall: 5.3 [3.0, 9.6]). The aRDs increased across age groups (aRD [95% CI] per 1,000 SARS-CoV-2-positive persons for 18-39: 10 [2, 18]; 40-64: 43 [33, 54]; 65 + : 84 [51, 116]; overall: 28 [21, 35]). CONCLUSIONS: Individuals with UHCs are at significantly increased risk of COVID-19-associated hospitalization regardless of age. Our findings support the prevention of severe COVID-19 in adults with UHCs in all age groups and in older adults aged 65 + years as ongoing local public health priorities.

Do the research priorities identified in SAGES Delphi studies resonate with rural general surgeons: a Washington state perspective.

BACKGROUND: Rural surgeons operate in an environment significantly different from that of their colleagues, and as such they face unique challenges. We hypothesized the Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) research agenda (as identified in the results of the 2014 Delphi study) will differ in its priorities from those identified by rural surgeons. We aimed to pilot a study in Washington state that could be replicated in other areas of the USA and the world. METHODS: We identified general surgeons working at rural critical access hospitals in the state of Washington. We then conducted virtual, semi-structured interviews and followed up with surveys and site visits. The survey included the 2014 SAGES Delphi-ranked research priorities. We asked rural surgeons to rank their top 5 of these 40 priorities and to detail any additional which were not on the list. RESULTS: We contacted 79 surgeons with a 30% response rate. We conducted 25 semi-structured interviews and received 18 completed follow-up surveys. These interviews were followed by site visits at 4 of the 23 sites. Of the original Delphi research priorities, those most cited by rural surgeons were #8 ("What is the best method for incorporating new techniques and technology for surgeons of variable levels of experience or training?") and #1 ("How do we best train, assess, and maintain proficiency of surgeons and surgical trainees in flexible endoscopy, laparoscopy, and open surgery?"). Four surgeons included the last SAGES priority (#40 "Is quality of life improved after ventral hernia repair?") among their top 5. CONCLUSION: This study suggests that although rural surgeons' research priorities align with the published SAGES Delphi survey, these surgeons rank the priorities differently. This may be because the predominant study population of the Delphi is SAGES membership who work in urban and academic centers. Plans for future SAGES Delphi survey could capture these unique priorities by intentional involvement of rural and community surgeons.

First Report of the Gastropod-Killing Nematode, Phasmarhabditis californica, in Washington State, U.S.A.

Phasmarhabditis californica, a commercially available biological control agent in England, Scotland, and Wales (Nemaslug 2.0 ®), was discovered for the first time in Washington State during 2022. Nematodes were recovered from the invasive gastropods Arion hortensis, Deroceras reticulatum, and Oxychilus sp. in garden centers in both Vancouver and Spokane. The 18S ribosomal RNA gene was used to identify the nematodes. This discovery builds upon previous reports of P. californica in California and Oregon and suggests that the species is widespread throughout the west coast of the U.S. Future research directions with P. californica are proposed.

Gun Violence is a Public Health Crisis in North Carolina: What Now?

Gun violence is an epidemic impacting the health and safety of North Carolinians. Mecklenburg County Public Health uses a public health approach to address this issue through four steps: 1) Define and monitor the problem, 2) Identify risk and protective factors, 3) Develop and test prevention strategies, 4) Assure widespread adoption.

Household Transmission of SARS-CoV-2 from Humans to Pets, Washington and Idaho, USA.

SARS-CoV-2 likely emerged from an animal reservoir. However, the frequency of and risk factors for interspecies transmission remain unclear. We conducted a community-based study in Idaho, USA, of pets in households that had >1 confirmed SARS-CoV-2 infections in humans. Among 119 dogs and 57 cats, clinical signs consistent with SARS-CoV-2 were reported for 20 dogs (21%) and 19 cats (39%). Of 81 dogs and 32 cats sampled, 40% of dogs and 43% of cats were seropositive, and 5% of dogs and 8% of cats were PCR positive. This discordance might be caused by delays in sampling. Respondents commonly reported close human‒animal contact and willingness to take measures to prevent transmission to their pets. Reported preventive measures showed a slightly protective but nonsignificant trend for both illness and seropositivity in pets. Sharing of beds and bowls had slight harmful effects, reaching statistical significance for sharing bowls and seropositivity.

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.