The Anopheles coluzzii range extends into Kenya: detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa

Background Anopheles coluzzii is a primary vector of malaria found in West and Central Africa, but its presence has hitherto never been documented in Kenya. A thorough understanding of vector bionomics is important as it enables the implementation of targeted and effective vector control interventions. Malaria vector surveillance efforts in the country have tended to focus on historically known primary vectors. The current study sought to determine the taxonomic status of samples collected from five different malaria epidemiological zones in Kenya as well as describe the population genetic structure and insecticide resistance profiles in relation to other An. coluzzii populations. Methods Mosquitoes were sampled as larvae from Busia, Kwale, Turkana, Kirinyaga and Kiambu counties, representing the range of malaria endemicities in Kenya, in 2019 and 2021 and emergent adults analysed using Whole Genome Sequencing (WGS) data processed in accordance with the Anopheles gambiae 1000 Genomes Project phase 3. Where available, historical samples from the same sites were included for WGS. Comparisons were made with An. coluzzii cohorts from West and Central Africa. Results This study reports the detection of An. coluzzii for the first time in Kenya. The species was detected in Turkana County across all three time points from which samples were analyzed and its presence confirmed through taxonomic analysis. Additionally, there was a lack of strong population genetic differentiation between An. coluzzii from Kenya and those from the more northerly regions of West and Central Africa, suggesting they represent a connected extension to the known species range. Mutations associated with target-site resistance to DDT and pyrethroids and metabolic resistance to DDT were found at high frequencies up to 64%. The profile and frequencies of the variants observed were similar to An. coluzzii from West and Central Africa but the ace-1 mutation linked to organophosphate and carbamate resistance present in An. coluzzii from coastal West Africa was absent in Kenya. Conclusions These findings emphasize the need for the incorporation of genomics in comprehensive and routine vector surveillance to inform on the range of malaria vector species, and their insecticide resistance status to inform the choice of effective vector control approaches

Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast

Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves : a retrospective genomic study

Background: Detailed understanding on SARS-CoV-2 regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic. Methods: Here, we analysed 1,139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction and virus dispersal between counties were estimated using discrete phylogeographic analysis. Results: During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; nine of which occurred in both waves, and four seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1 and N.8). Most of the sequenced infections belonged to lineage B.1 (n=723, 63%) which predominated in both Wave 1 (73%, followed by lineages N.8 (6%) and B.1.1 (6%)) and Wave 2 (56%, followed by lineages B.1.549 (21%) and B.1.530 (5%). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many COVID-19 government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity. Conclusions: Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Does Insurance Source Make a Difference In Meeting Rehabilitation Goals in Skilled Nursing Facilities?

Introduction The objective of this study was to determine whether there was an association between attainment of the Skilled Nursing Facility (SNF) goals and the payer source. Three insurance sources (Medicare, County contracts and Commercial insurances) were evaluated across 3 urban SNFs. Because each insurance source had different provider regulations, we investigated the potential impact of these differences on rehabilitation outcomes. Method We conducted a retrospective study of 234 patients admitted in three SNFs. Information collected included baseline characteristics (age, gender, etc.) as well as whether physical therapy, wound care and intravenous antibiotics goals were achieved. An “all or none” attainment of SNF goals analysis was measured using the Poisson logistic regression adjusting for age, gender, diabetes mellitus, anemia, infections and grooming as the baseline functional status at SNF admission. Results The mean ages of Medicare, Commercial insurance and County Contract patients were 73, 66 and 47 years old and the median SNF care length of stay was 52, 37 and 23 days respectively. When compared to Medicare, Commercial insurance patients [RR 2.51 (1.33 – 4.73)] were more likely to achieve their physical therapy goals, whereas County contract patients showed no difference in attaining physical therapy goals when compared to Medicare patients. Subset analyses revealed that older patients (p = 0.02), diabetics (p=0.03), patients with infections (p=0.03), those with a low functional status (p=0.03) and females (p=0.02) were less likely to attain predicted rehabilitation goals. Conclusion Commercial insurance patients are more likely to attain SNF care goals compared to Medicare patients. This study indicates that factors such as age, gender and the baseline functional status, in addition to diabetes mellitus and infections influence attainment of SNF care goals. Also noted is the week-to-week threat of Commercial insurance discontinuation if no rehabilitation progress is made, thus suggesting that time limitations for recovery specified by an insurer may be a motivating force for accelerating the recovery process

Examining inequalities in spatial access to national health insurance fund contracted facilities in Kenya

Abstract Background Kenya aims to achieve universal health coverage (UHC) by 2030 and has selected the National Health Insurance Fund (NHIF) as the ‘vehicle’ to drive the UHC agenda. While there is some progress in moving the country towards UHC, the availability and accessibility to NHIF-contracted facilities may be a barrier to equitable access to care. We estimated the spatial access to NHIF-contracted facilities in Kenya to provide information to advance the UHC agenda in Kenya. Methods We merged NHIF-contracted facility data to the geocoded inventory of health facilities in Kenya to assign facility geospatial locations. We combined this database with covariates data including road network, elevation, land use, and travel barriers. We estimated the proportion of the population living within 60- and 120-minute travel time to an NHIF-contracted facility at a 1-x1-kilometer spatial resolution nationally and at county levels using the WHO AccessMod tool. Results We included a total of 3,858 NHIF-contracted facilities. Nationally, 81.4% and 89.6% of the population lived within 60- and 120-minute travel time to an NHIF-contracted facility respectively. At the county level, the proportion of the population living within 1-hour of travel time to an NHIF-contracted facility ranged from as low as 28.1% in Wajir county to 100% in Nyamira and Kisii counties. Overall, only four counties (Kiambu, Kisii, Nairobi and Nyamira) had met the target of having 100% of their population living within 1-hour (60 min) travel time to an NHIF-contracted facility. On average, it takes 209, 210 and 216 min to travel to an NHIF-contracted facility, outpatient and inpatient facilities respectively. At the county level, travel time to an NHIF-contracted facility ranged from 10 min in Vihiga County to 333 min in Garissa. Conclusion Our study offers evidence of the spatial access estimates to NHIF-contracted facilities in Kenya that can inform contracting decisions by the social health insurer, especially focussing on marginalised counties where more facilities need to be contracted. Besides, this evidence will be crucial as the country gears towards accelerating progress towards achieving UHC using social health insurance as the strategy to drive the UHC agenda in Kenya

Blunted IL17/IL22 and pro-inflammatory cytokine responses in the genital tract and blood of HIV-exposed, seronegative female sex workers in Kenya.

Identifying the immune correlates of reduced susceptibility to HIV remains a key goal for the HIV vaccine field, and individuals who are HIV-exposed, seronegative (HESN) may offer important clues. Reduced systemic immune activation has been described in HESN individuals. Conversely, pro-inflammatory T cell subsets, particularly CD4+ T cells producing the cytokine IL17 (Th17 cells), may represent a highly susceptible target for HIV infection after sexual exposure. Therefore, we characterized the cellular pro-inflammatory and IL17/IL22 cytokine immune milieu in the genital mucosa and blood of HESN female sex workers (FSWs).Blinded lab personnel characterized basal and mitogen-induced gene and cytokine immune responses in the cervix and blood of HESN FSWs (n = 116) and non-FSW controls (n = 17) using qPCR and ELISA. IL17 and IL22 production was significantly reduced in both the cervix and blood of HESNs, both in resting cells and after mitogen stimulation. In addition, HESN participants demonstrated blunted production of both pro-inflammatory cytokines and β-chemokines.We conclude that HIV exposure without infection was associated with blunted IL17/IL22 and pro-inflammatory responses, both systemically and at the site of mucosal HIV exposure. It will be important for further studies to examine the causal nature of the association and to define the cell subsets responsible for these differences

Additional file 1: of Effects of HIV-1 infection on malaria parasitemia in milo sub-location, western Kenya

Table S1. Expressions age, sex, malaria parasitaemia and density against HIV status

The HAART cell phone adherence trial (WelTel Kenya1): a randomized controlled trial protocol

Background: The objectives are to compare the effectiveness of cell phone-supported SMS messaging to standard care on adherence, quality of life, retention, and mortality in a population receiving antiretroviral therapy (ART) in Nairobi, Kenya. Methods and Design: A multi-site randomized controlled open-label trial. A central randomization centre provided opaque envelopes to allocate treatments. Patients initiating ART at three comprehensive care clinics in Kenya will be randomized to receive either a structured weekly SMS ('short message system' or text message) slogan (the intervention) or current standard of care support mechanisms alone (the control). Our hypothesis is that using a structured mobile phone protocol to keep in touch with patients will improve adherence to ART and other patient outcomes. Participants are evaluated at baseline, and then at six and twelve months after initiating ART. The care providers keep a weekly study log of all phone based communications with study participants. Primary outcomes are self-reported adherence to ART and suppression of HIV viral load at twelve months scheduled follow-up. Secondary outcomes are improvements in health, quality of life, social and economic factors, and retention on ART. Primary analysis is by 'intention-to-treat'. Sensitivity analysis will be used to assess per-protocol effects. Analysis of covariates will be undertaken to determine factors that contribute or deter from expected and determined outcomes. Discussion: This study protocol tests whether a novel structured mobile phone intervention can positively contribute to ART management in a resource-limited setting. Trial Registration: Trial Registration Number: NCT00830622Other UBCReviewedFacult