SCALE-UP II: protocol for a pragmatic randomised trial examining population health management interventions to increase the uptake of at-home COVID-19 testing in community health centres.

INTRODUCTION: SCALE-UP II aims to investigate the effectiveness of population health management interventions using text messaging (TM), chatbots and patient navigation (PN) in increasing the uptake of at-home COVID-19 testing among patients in historically marginalised communities, specifically, those receiving care at community health centres (CHCs). METHODS AND ANALYSIS: The trial is a multisite, randomised pragmatic clinical trial. Eligible patients are >18 years old with a primary care visit in the last 3 years at one of the participating CHCs. Demographic data will be obtained from CHC electronic health records. Patients will be randomised to one of two factorial designs based on smartphone ownership. Patients who self-report replying to a text message that they have a smartphone will be randomised in a 2×2×2 factorial fashion to receive (1) chatbot or TM; (2) PN (yes or no); and (3) repeated offers to interact with the interventions every 10 or 30 days. Participants who do not self-report as having a smartphone will be randomised in a 2×2 factorial fashion to receive (1) TM with or without PN; and (2) repeated offers every 10 or 30 days. The interventions will be sent in English or Spanish, with an option to request at-home COVID-19 test kits. The primary outcome is the proportion of participants using at-home COVID-19 tests during a 90-day follow-up. The study will evaluate the main effects and interactions among interventions, implementation outcomes and predictors and moderators of study outcomes. Statistical analyses will include logistic regression, stratified subgroup analyses and adjustment for stratification factors. ETHICS AND DISSEMINATION: The protocol was approved by the University of Utah Institutional Review Board. On completion, study data will be made available in compliance with National Institutes of Health data sharing policies. Results will be disseminated through study partners and peer-reviewed publications. TRIAL REGISTRATION NUMBER: ClinicalTrials.gov: NCT05533918 and NCT05533359.

Increasing the reach of evidence-based interventions for weight management and diabetes prevention among Medicaid patients: study protocol for a pilot Sequential Multiple Assignment Randomised Trial.

INTRODUCTION: Over 40% of US adults meet criteria for obesity, a major risk factor for chronic disease. Obesity disproportionately impacts populations that have been historically marginalised (eg, low socioeconomic status, rural, some racial/ethnic minority groups). Evidence-based interventions (EBIs) for weight management exist but reach less than 3% of eligible individuals. The aims of this pilot randomised controlled trial are to evaluate feasibility and acceptability of dissemination strategies designed to increase reach of EBIs for weight management. METHODS AND ANALYSIS: This study is a two-phase, Sequential Multiple Assignment Randomized Trial, conducted with 200 Medicaid patients. In phase 1, patients will be individually randomised to single text message (TM1) or multiple text messages (TM+). Phase 2 is based on treatment response. Patients who enrol in the EBI within 12 weeks of exposure to phase 1 (ie, responders) receive no further interventions. Patients in TM1 who do not enrol in the EBI within 12 weeks of exposure (ie, TM1 non-responders) will be randomised to either TM1-Continued (ie, no further TM) or TM1 & MAPS (ie, no further TM, up to 2 Motivation And Problem Solving (MAPS) navigation calls) over the next 12 weeks. Patients in TM+ who do not enrol in the EBI (ie, TM+ non-responders) will be randomised to either TM+Continued (ie, monthly text messages) or TM+ & MAPS (ie, monthly text messages, plus up to 2 MAPS calls) over the next 12 weeks. Descriptive statistics will be used to characterise feasibility (eg, proportion of patients eligible, contacted and enrolled in the trial) and acceptability (eg, participant opt-out, participant engagement with dissemination strategies, EBI reach (ie, the proportion of participants who enrol in EBI), adherence, effectiveness). ETHICS AND DISSEMINATION: Study protocol was approved by the University of Utah Institutional Review Board (#00139694). Results will be disseminated through study partners and peer-reviewed publications. TRIAL REGISTRATION NUMBER: clinicaltrials.gov; NCT05666323.

Preliminary Reach of an Information Technology Approach to Support COVID-19 Testing in Schools.

OBJECTIVES: SCALE-UP Counts tests population health management interventions to promote coronavirus disease 2019 (COVID-19) testing in kindergarten through 12th-grade schools that serve populations that have been historically marginalized. METHODS: Within 6 participating schools, we identified 3506 unique parents/guardians who served as the primary contact for at least 1 student. Participants were randomized to text messaging (TM), text messaging + health navigation (HN) (TM + HN), or usual care. Bidirectional texts provided COVID-19 symptom screening, along with guidance on obtaining and using tests as appropriate. If parents/guardians in the TM + HN group were advised to test their child but either did not test or did not respond to texts, they were called by a trained health navigator to address barriers. RESULTS: Participating schools served a student population that was 32.9% non-white and 15.4% Hispanic, with 49.6% of students eligible to receive free lunches. Overall, 98.8% of parents/guardians had a valid cell phone, of which 3.8% opted out. Among the 2323 parents/guardians included in the intervention, 79.6% (n = 1849) were randomized to receive TM, and 19.1% (n = 354) engaged with TM (ie, responded to at least 1 message). Within the TM + HN group (40.1%, n = 932), 1.3% (n = 12) qualified for HN at least once, of which 41.7% (n = 5) talked to a health navigator. CONCLUSIONS: TM and HN are feasible ways to reach parents/guardians of kindergarten through 12th-grade students to provide COVID-19 screening messages. Strategies to improve engagement may strengthen the impact of the intervention.

Rapid-cycle designs to adapt interventions for COVID-19 in safety-net healthcare systems.

Racial/ethnic minority, low socioeconomic status, and rural populations are disproportionately affected by COVID-19. Developing and evaluating interventions to address COVID-19 testing and vaccination among these populations are crucial to improving health inequities. The purpose of this paper is to describe the application of a rapid-cycle design and adaptation process from an ongoing trial to address COVID-19 among safety-net healthcare system patients. The rapid-cycle design and adaptation process included: (a) assessing context and determining relevant models/frameworks; (b) determining core and modifiable components of interventions; and (c) conducting iterative adaptations using Plan-Do-Study-Act (PDSA) cycles. PDSA cycles included: Plan. Gather information from potential adopters/implementers (e.g., Community Health Center [CHC] staff/patients) and design initial interventions; Do. Implement interventions in single CHC or patient cohort; Study. Examine process, outcome, and context data (e.g., infection rates); and, Act. If necessary, refine interventions based on process and outcome data, then disseminate interventions to other CHCs and patient cohorts. Seven CHC systems with 26 clinics participated in the trial. Rapid-cycle, PDSA-based adaptations were made to adapt to evolving COVID-19-related needs. Near real-time data used for adaptation included data on infection hot spots, CHC capacity, stakeholder priorities, local/national policies, and testing/vaccine availability. Adaptations included those to study design, intervention content, and intervention cohorts. Decision-making included multiple stakeholders (e.g., State Department of Health, Primary Care Association, CHCs, patients, researchers). Rapid-cycle designs may improve the relevance and timeliness of interventions for CHCs and other settings that provide care to populations experiencing health inequities, and for rapidly evolving healthcare challenges such as COVID-19.

Racial/ethnic minority, low socioeconomic status, and rural populations experience a disproportionate burden of COVID-19. Finding ways to address COVID-19 among these populations is crucial to improving health inequities. The purpose of this paper is to describe the rapid-cycle design process for a research project to address COVID-19 testing and vaccination among safety-net healthcare system patients. The project used real-time information on changes in COVID-19 policy (e.g., vaccination authorization), local case rates, and the capacity of safety-net healthcare systems to iteratively change interventions to ensure interventions were relevant and timely for patients. Key changes that were made to interventions included a change to the study design to include vaccination as a focus of the interventions after the vaccine was authorized; change in intervention content according to the capacity of local Community Health Centers to provide testing to patients; and changes to intervention cohorts such that priority groups of patients were selected for intervention based on characteristics including age, residency in an infection "hot spot," or race/ethnicity. Iteratively improving interventions based on real-time data collection may increase intervention relevance and timeliness, and rapid-cycle adaptions can be successfully implemented in resource constrained settings like safety-net healthcare systems.

Mortality by ribosomal sequencing (MoRS) provides a window into taxon-specific cell lysis.

Microbes are by far the dominant biomass in the world's oceans and drive biogeochemical cycles that are critical to life on Earth. The composition of marine microbial communities is highly dynamic, spatially and temporally, with consequent effects on their functional roles. In part, these changes in composition result from viral lysis, which is taxon-specific and estimated to account for about half of marine microbial mortality. Here, we show that extracellular ribosomal RNA (rRNAext) is produced by viral lysis, and that specific lysed populations can be identified by sequencing rRNAext recovered from seawater samples. In ten seawater samples collected at five depths between the surface and 265 m during and following a phytoplankton bloom, lysis was detected in about 15% of 16,946 prokaryotic taxa, identified from amplicon sequence variants (ASVs), with lysis occurring in up to 34% of taxa within a water sample. The ratio of rRNAext to cellular rRNA (rRNAcell) was used as an index of taxon-specific lysis, and revealed that higher relative lysis was most commonly associated with copiotrophic bacteria that were in relatively low abundance, such as those in the genera Escherichia and Shigella spp., as well as members of the Bacteriodetes; whereas, relatively low lysis was more common in taxa that are often relatively abundant, such as members of the Pelagibacterales (i.e., SAR11 clade), cyanobacteria in the genus Synechococcus, and members of the phylum Thaumarchaeota (synonym, Nitrososphaerota) that comprised about 13-15% of the 16 S rRNA gene sequences below 30 m. These results provide an explanation for the long-standing conundrum of why highly productive bacteria that are readily isolated from seawater are often in very low abundance. The ability to estimate taxon-specific cell lysis will help explore the distribution and abundance of microbial populations in nature.

Viruses in Subsurface Environments.

Over the past 20 years, our knowledge of virus diversity and abundance in subsurface environments has expanded dramatically through application of quantitative metagenomic approaches. In most subsurface environments, viral diversity and abundance rival viral diversity and abundance observed in surface environments. Most of these viruses are uncharacterized in terms of their hosts and replication cycles. Analysis of accessory metabolic genes encoded by subsurface viruses indicates that they evolved to replicate within the unique features of their environments. The key question remains: What role do these viruses play in the ecology and evolution of the environments in which they replicate? Undoubtedly, as more virologists examine the role of viruses in subsurface environments, new insights will emerge.

"When She Says Daddy": Black Fathers' Recidivism following Reentry from Jail.

We report on the findings of a mixed methods longitudinal study of 84 African American fathers of young children who were enrolled into the study during the father's jail stay. Participants were assessed using interviews, self-report measures, and administrative records on frequency of father-child contact, father-caregiver relationship quality, family support, paternal pre-incarceration employment, fathers' plans to live with the child upon reentry, history of substance abuse, and new convictions one year following release from jail. Qualitative analysis revealed three primary identities of fathers during incarceration: father as nurturer, father as protector, and father as provider. Qualitative analysis of interview data detailed the ways in which the context of incarceration and the presence of the criminal justice system interacts with these identities to impact family structure, parent-child visits, plans for release, and motivation for desistance. Quantitative analysis indicated heterogeneity among fathers, with links between parent-child contact and desistance conditional on fathers' plans for coresidence with children as well as family support and relationship quality. Taken together, the findings highlight the strengths of African American fathers and their families despite the risks associated with incarceration, including the importance of family support and children as motivation for desistance. The results have implications for how the justice system weighs the bidirectional influences of fathers and families.

Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B.

UNLABELLED: Here we present the first genomic characterization of viruses infecting Nostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infect Nostoc sp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids of Cyanothece sp. strain PCC 7424, Nostoc sp. strain PCC 7120, and Anabaena variabilis ATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome of Nostoc sp. strain PCC 7524. The Nostoc cyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages. IMPORTANCE: Filamentous cyanobacteria belonging to the genus Nostoc are widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis.

Understanding of viral assemblage structure in natural environments remains a daunting task. Total viral assemblage sequencing (for example, viral metagenomics) provides a tractable approach. However, even with the availability of next-generation sequencing technology it is usually only possible to obtain a fragmented view of viral assemblages in natural ecosystems. In this study, we applied a network-based approach in combination with viral metagenomics to investigate viral assemblage structure in the high temperature, acidic hot springs of Yellowstone National Park, USA. Our results show that this approach can identify distinct viral groups and provide insights into the viral assemblage structure. We identified 110 viral groups in the hot springs environment, with each viral group likely representing a viral family at the sub-family taxonomic level. Most of these viral groups are previously unknown DNA viruses likely infecting archaeal hosts. Overall, this study demonstrates the utility of combining viral assemblage sequencing approaches with network analysis to gain insights into viral assemblage structure in natural ecosystems.

Development of a genetic system for the archaeal virus Sulfolobus turreted icosahedral virus (STIV).

Our understanding of archaeal viruses has been limited by the lack of genetic systems for examining viral function. We describe the construction of an infectious clone for the archaeal virus Sulfolobus turreted icosahedral virus (STIV). STIV was isolated from a high temperature (82°C) acidic (pH 2.2) hot spring in Yellowstone National Park and replicates in the archaeal model organism Sulfolobus solfataricus (Rice et al., 2004). While STIV is one of most studied archaeal viruses, little is known about its replication cycle. The development of an STIV infectious clone allows for directed gene disruptions and detailed genetic analysis of the virus. The utility of the STIV infectious clone was demonstrated by gene disruption of STIV open reading frame (ORF) B116 which resulted in crippled virus replication, while disruption of ORFs A197, C381 and B345 was lethal for virus replication.