Trends and factors associated with HIV viral load non-suppression among treatment-experienced female sex workers in Kenya: a retrospective cohort study.

Background: Transactional sexual relations in the absence of condom use is a well-established behaviour that strongly contributes to HIV transmission if the infected person is not virally suppressed. In this study, we determined the trends and factors associated with VLNS among treatment-experienced FSWs in Kenya.

Methods: This retrospective cohort study used data collected from 7-sex workers outreach clinics between 2015 and 2022.

Assessment of neonatal referral infrastructure and clinical characteristics of referred neonates in three first referral hospitals in Nairobi County, Kenya.

Background: One in five newborns in Nairobi County, Kenya, may require inpatient neonatal care. We sought to examine referrals to and from three busy first-level referral public hospitals in Nairobi and what infrastructure and systems are available to support neonatal transport from these first-referral level hospitals to the main tertiary care center.

Methods: Patient-level data of newborns over 12 months were retrospectively extracted from routinely collected patient data and examined to characterize those referred into and out of three newborn units in the study hospitals.

Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.

Background: Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context.

Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient.

Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats.

COVID-19 pandemic effects on neonatal inpatient admissions and mortality: interrupted time series analysis of facilities implementing NEST360 in Kenya, Malawi, Nigeria, and Tanzania.

Background: The emergence of COVID-19 precipitated containment policies (e.g., lockdowns, school closures, etc.

Quantifying health facility service readiness for small and sick newborn care: comparing standards-based and WHO level-2 + scoring for 64 hospitals implementing with NEST360 in Kenya, Malawi, Nigeria, and Tanzania.

Background: Service readiness tools are important for assessing hospital capacity to provide quality small and sick newborn care (SSNC). Lack of summary scoring approaches for SSNC service readiness means we are unable to track national targets such as the Every Newborn Action Plan targets.

Methods: A health facility assessment (HFA) tool was co-designed by Newborn Essential Solutions and Technologies (NEST360) and UNICEF with four African governments.

Health facility assessment of small and sick newborn care in low- and middle-income countries: systematic tool development and operationalisation with NEST360 and UNICEF.

Background: Each year an estimated 2.3 million newborns die in the first 28 days of life. Most of these deaths are preventable, and high-quality neonatal care is fundamental for surviving and thriving.

Factors associated with viral load non-suppression among treatment-experienced pre-teenage children living with HIV in Kenya: a nationwide population-based cohort study, 2015-2021.

Background: Viral load non-suppression (VLNS) in children is a major public health concern because of attendant HIV disease progression and risk of morbidity and mortality. Based on a nationally representative database we present estimates of the prevalence, trends and factors associated with VLNS in Kenyan pre-teenage children between 2015 and 2021.

Methods: Kenya National AIDS & STI Control Program's (NASCOP) maintains an early infant diagnosis and viral load (EID/VL) database for all persons living with HIV who are enrolled in the country's primary care clinics for purposes of monitoring progress towards achievement of the 95% viral suppression goals.

Neonatal inpatient dataset for small and sick newborn care in low- and middle-income countries: systematic development and multi-country operationalisation with NEST360.

Background: Every Newborn Action Plan (ENAP) coverage target 4 necessitates national scale-up of Level-2 Small and Sick Newborn Care (SSNC) (with Continuous Positive Airway Pressure (CPAP)) in 80% of districts by 2025. Routine neonatal inpatient data is important for improving quality of care, targeting equity gaps, and enabling data-driven decision-making at individual, district, and national-levels. Existing neonatal inpatient datasets vary in purpose, size, definitions, and collection processes.

Development of a small and sick newborn clinical audit tool and its implementation guide using a human-centred design approach newborn clinical audit process and design.

Clinical audits are an important intervention that enables health workers to reflect on their practice and identify and act on modifiable gaps in the care provided. To effectively audit the quality of care provided to the small and sick newborns, the clinical audit process must use a structured tool that comprehensively covers the continuum of newborn care from immediately after birth to the period of newborn unit care. The objective of the study was to co-design a newborn clinical audit tool that considered the key principles of a Human Centred Design approach.

Improving in-patient neonatal data quality as a pre-requisite for monitoring and improving quality of care at scale: A multisite retrospective cohort study in Kenya.

The objectives of this study were to (1)explore the quality of clinical data generated from hospitals providing in-patient neonatal care participating in a clinical information network (CIN) and whether data improved over time, and if data are adequate, (2)characterise accuracy of prescribing for basic treatments provided to neonatal in-patients over time. This was a retrospective cohort study involving neonates ≤28 days admitted between January 2018 and December 2021 in 20 government hospitals with an interquartile range of annual neonatal inpatient admissions between 550 and 1640 in Kenya. These hospitals participated in routine audit and feedback processes on quality of documentation and care over the study period.

Preoperative Management of Medications for Rheumatologic and HIV Diseases: Society for Perioperative Assessment and Quality Improvement (SPAQI) Consensus Statement.

Perioperative medical management is challenging because of the rising complexity of patients presenting for surgical procedures. A key part of preoperative optimization is appropriate management of long-term medications, yet guidelines and consensus statements for perioperative medication management are lacking. Available resources use recommendations derived from individual studies and do not include a multidisciplinary focus on formal consensus.

Diversity and ecological footprint of Global Ocean RNA viruses.

DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their ecological impacts from pole to pole.

Evaluation of an audit and feedback intervention to reduce gentamicin prescription errors in newborn treatment (ReGENT) in neonatal inpatient care in Kenya: a controlled interrupted time series study protocol.

Background: Medication errors are likely common in low- and middle-income countries (LMICs). In neonatal hospital care where the population with severe illness has a high mortality rate, around 14.9% of drug prescriptions have errors in LMICs settings.

Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome.

Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding.

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation.

Background: Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization.

A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya.

Common bean (.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production.

Evolutionary insights of and .

Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea.

Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya.

Sweet potato is a major food security crop within sub-Saharan Africa where 90% of Africa production occurs. One of the major limitations of sweet potato production are viral infections. In this study, we used a combination of whole genome sequences from a field isolate obtained from Kenya and those available in GenBank.