Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya

Genomic surveillance and identification of COVID-19 outbreaks are important in understanding the genetic diversity, phylogeny, and lineages of SARS-CoV-2. Genomic surveillance provides insights into circulating infections, and the robustness and design of vaccines and other infection control approaches. We sequenced 57 SARS-CoV-2 isolates from a Kenyan clinical population, of which 55 passed quality checks using the Ultrafast Sample placement on the Existing tRee (UShER) workflow. Phylo-genome-temporal analyses across two regions in Kenya (Nairobi and Kiambu County) revealed that B.1.1.7 (Alpha; n = 32, 56.1%) and B.1 (n = 9, 15.8%) were the predominant lineages, exhibiting low Ct values (5-31) suggesting high infectivity, and variant mutations across the two regions. Lineages B.1.617.2, B.1.1, A.23.1, A.2.5.1, B.1.596, A, and B.1.405 were also detected across sampling sites within target populations. The lineages and genetic isolates were traced back to China (A), Costa Rica (A.2.5.1), Europe (B.1, B.1.1, A.23.1), the USA (B.1.405, B.1.596), South Africa (B.1.617.2), and the United Kingdom (B.1.1.7), indicating multiple introduction events. This study represents one of the genomic SARS-CoV-2 epidemiology studies in the Nairobi metropolitan area, and describes the importance of continued surveillance for pandemic control

Hypothermia amongst neonatal admissions in Kenya: a retrospective cohort study assessing prevalence, trends, associated factors, and its relationship with all-cause neonatal mortality

BackgroundReports on hypothermia from high-burden countries like Kenya amongst sick newborns often include few centers or relatively small sample sizes.ObjectivesThis study endeavored to describe: (i) the burden of hypothermia on admission across 21 newborn units in Kenya, (ii) any trend in prevalence of hypothermia over time, (iii) factors associated with hypothermia at admission, and (iv) hypothermia's association with inpatient neonatal mortality.MethodsA retrospective cohort study was conducted from January 2020 to March 2023, focusing on small and sick newborns admitted in 21 NBUs. The primary and secondary outcome measures were the prevalence of hypothermia at admission and mortality during the index admission, respectively. An ordinal logistic regression model was used to estimate the relationship between selected factors and the outcomes cold stress (36.0°C–36.4°C) and hypothermia (<36.0°C). Factors associated with neonatal mortality, including hypothermia defined as body temperature below 36.0°C, were also explored using logistic regression.ResultsA total of 58,804 newborns from newborn units in 21 study hospitals were included in the analysis. Out of these, 47,999 (82%) had their admission temperature recorded and 8,391 (17.5%) had hypothermia. Hypothermia prevalence decreased over the study period while admission temperature documentation increased. Significant associations were found between low birthweight and very low (0–3) APGAR scores with hypothermia at admission. Odds of hypothermia reduced as ambient temperature and month of participation in the Clinical Information Network (a collaborative learning health platform for healthcare improvement) increased. Hypothermia at admission was associated with 35% (OR 1.35, 95% CI 1.22, 1.50) increase in odds of neonatal inpatient death.ConclusionsA substantial proportion of newborns are admitted with hypothermia, indicating a breakdown in warm chain protocols after birth and intra-hospital transport that increases odds of mortality. Urgent implementation of rigorous warm chain protocols, particularly for low-birth-weight babies, is crucial to protect these vulnerable newborns from the detrimental effects of hypothermia

Table_2_Genetic variation of the Plasmodium falciparum circumsporozoite protein in parasite isolates from Homabay County in Kenya.xls

The Plasmodium falciparum Circumsporozoite Protein (PfCSP) has been used in developing the RTS,S, and R21 malaria vaccines. However, genetic polymorphisms within Pfcsp compromise the effectiveness of the vaccine. Thus, it is essential to continuously assess the genetic diversity of Pfcsp, especially when deploying it across different geographical regions. In this study, we assessed the genetic diversity of the Pfcsp on isolates from Homabay County, a malaria-endemic region in western Kenya, and compared it against other isolates from Kenya. We extracted DNA from 27 microscopically confirmed P. falciparum positive samples and conducted Illumina sequencing to generate paired-end short reads. The sequences were then mapped to the Pf3D7 reference genome, and genetic variation was analyzed using bcftools. Additionally, we retrieved isolates from two other malaria-endemic regions in Kenya, Kisumu (n=58) and Kilifi (n=596), from MalariaGEN version 7 and compared their genetic diversity and natural selection. We also evaluated the predicted binding affinities for HLA class I and II supertype alleles for the identified haplotypes using NetMHCpan and NetMHCIIpan. Our results show that the N-terminal of PfCSP was relatively conserved with a notable mutation at A98G across all isolates. The number of NANP repeats varied across the three Kenyan sites within the central repeat region. Furthermore, the C-terminal region showed polymorphism within the Th2R and Th3R regions. Haplotype network analysis of the Kenyan isolates revealed 69 haplotypes, with the 3D7 reference being found in the most prevalent haplotype. When assessing the predicted binding affinities between supertypes in HLA class I and II with the identified haplotypes, we observed stronger predicted binding affinities to multiple haplotypes except for those containing the 3D7 reference. The results suggest the need to take into account the existing changes occurring in Pfcsp while developing malaria vaccines.</p

Table_1_Genetic variation of the Plasmodium falciparum circumsporozoite protein in parasite isolates from Homabay County in Kenya.xlsx

The Plasmodium falciparum Circumsporozoite Protein (PfCSP) has been used in developing the RTS,S, and R21 malaria vaccines. However, genetic polymorphisms within Pfcsp compromise the effectiveness of the vaccine. Thus, it is essential to continuously assess the genetic diversity of Pfcsp, especially when deploying it across different geographical regions. In this study, we assessed the genetic diversity of the Pfcsp on isolates from Homabay County, a malaria-endemic region in western Kenya, and compared it against other isolates from Kenya. We extracted DNA from 27 microscopically confirmed P. falciparum positive samples and conducted Illumina sequencing to generate paired-end short reads. The sequences were then mapped to the Pf3D7 reference genome, and genetic variation was analyzed using bcftools. Additionally, we retrieved isolates from two other malaria-endemic regions in Kenya, Kisumu (n=58) and Kilifi (n=596), from MalariaGEN version 7 and compared their genetic diversity and natural selection. We also evaluated the predicted binding affinities for HLA class I and II supertype alleles for the identified haplotypes using NetMHCpan and NetMHCIIpan. Our results show that the N-terminal of PfCSP was relatively conserved with a notable mutation at A98G across all isolates. The number of NANP repeats varied across the three Kenyan sites within the central repeat region. Furthermore, the C-terminal region showed polymorphism within the Th2R and Th3R regions. Haplotype network analysis of the Kenyan isolates revealed 69 haplotypes, with the 3D7 reference being found in the most prevalent haplotype. When assessing the predicted binding affinities between supertypes in HLA class I and II with the identified haplotypes, we observed stronger predicted binding affinities to multiple haplotypes except for those containing the 3D7 reference. The results suggest the need to take into account the existing changes occurring in Pfcsp while developing malaria vaccines.</p

Neonatal mortality in Kenyan hospitals: a multisite, retrospective, cohort study

Background Most of the deaths among neonates in low-income and middle-income countries (LMICs) can be prevented through universal access to basic high-quality health services including essential facility-based inpatient care. However, poor routine data undermines data-informed efforts to monitor and promote improvements in the quality of newborn care across hospitals.Methods Continuously collected routine patients’ data from structured paper record forms for all admissions to newborn units (NBUs) from 16 purposively selected Kenyan public hospitals that are part of a clinical information network were analysed together with data from all paediatric admissions ages 0–13 years from 14 of these hospitals. Data are used to show the proportion of all admissions and deaths in the neonatal age group and examine morbidity and mortality patterns, stratified by birth weight, and their variation across hospitals.Findings During the 354 hospital months study period, 90 222 patients were admitted to the 14 hospitals contributing NBU and general paediatric ward data. 46% of all the admissions were neonates (aged 0–28 days), but they accounted for 66% of the deaths in the age group 0–13 years. 41 657 inborn neonates were admitted in the NBUs across the 16 hospitals during the study period. 4266/41 657 died giving a crude mortality rate of 10.2% (95% CI 9.97% to 10.55%), with 60% of these deaths occurring on the first-day of admission. Intrapartum-related complications was the single most common diagnosis among the neonates with birth weight of 2000 g or more who died. A threefold variation in mortality across hospitals was observed for birth weight categories 1000–1499 g and 1500–1999 g.Interpretation The high proportion of neonatal deaths in hospitals may reflect changing patterns of childhood mortality. Majority of newborns died of preventable causes (&gt;95%). Despite availability of high-impact low-cost interventions, hospitals have high and very variable mortality proportions after stratification by birth weight