Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Kuja JO

PROVIDER: S-EPMC9434529 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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

Kuja Josiah O JO Kanoi Bernard N BN Balboa Renzo F RF Shiluli Clement C Maina Michael M Waweru Harrison H Gathii Kimita K Mungai Mary M Masika Moses M Anzala Omu O Mwau Matilu M Clark Taane G TG Waitumbi John J Gitaka Jesse J

BMC genomics 20220901 1

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-t ...[more]

PMID: 36050650

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Project description:BackgroundThe double burden of diabetes mellitus (DM) and pulmonary tuberculosis (TB) is one of the global health challenges. Studies done in different parts of the world indicate that 12%-44% of TB disease is associated with DM. In Kenya TB-DM co-morbidity data is scarce and is not readily available. In this study we set to determine the difference in treatment outcomes among TB and TB/DM comorbidity patients and their respective clinical and socio-demographic characteristics.ObjectiveTo determine prognostic factors among TB and TB/DM comorbidity among patients on short course regimen within Nairobi and Kiambu counties in Kenya.MethodsWe carried out a prospective cohort study of non-pregnant patients aged 15 years and above that tested positive for TB in two peri‑urban counties in Kenya between February 2014 and August 2015. Clinical and socio demographic data were obtained from a questionnaire and medical records of the National TB program patient data base at two, three, five and six months. The data consisted of TB status, HIV status, TB lineage, County, (Glucose, %HbA1c, creatinine) weight, height, BMI, regimen, sex, level of education, employment status, distance from health facility, number of cigarettes smoked, home size, and diet. Univariate analysis was then used to compare each potential risk factor in the TB and TB/DM patients by the Pearson x2 test of proportions or fisher exact test, as appropriate.ResultsDM prevalence (HbA1c > 6%) among TB infected patients was 37.2%. Regimen, employment status, alcohol intake, smoking, age and household size were some of the factors associated with DM among TB patients at p-value < 0.05. The number of cigarettes smoked per day and the value of the BUN were significant risk factors of developing DM among TB patients (p values = 0.045). Mean time to conversion from positive to negative was slightly higher for the TB-DM patients compared to the TB patents, though not statistically significant (p = 0.365).ConclusionPatients regimen, employment status, alcohol intake, smoking, age and are associated with DM among TB patients.

Project description:Naivasha thorn tree, Acacia xanthophloea, is grown for foliage, timber, shade and rehabilitation of soils in areas with high water tables in Kenya. Its production is threatened by insect pests, which cause major losses. Very little is documented on wood-boring beetles which cause considerable economic damage to lumber used in a variety of applications, and little is known about their natural enemies in Kenya. We conducted the study to evaluate the occurrence of wood-boring beetles on A. xanthophloea in two different regions of Kenya. Infested wood samples of A. xanthophloea with fresh exit holes were collected from three sites in Kenyatta University (KU), Nairobi and Mitaboni in Machakos, Kenya. The samples were placed in clear plastic buckets and kept at ambient temperatures 23±2°C, 65±10% relative humidity and 12L: 12D in a laboratory where they were observed daily for adult emergence. Adult beetles were collected every three days for identification and data recording. The experiment was replicated four times and data collected twice a week for 6 months. Data on abundance was subjected to analysis of variance using SAS software. A total of 5,850 and 4,691 beetles were collected where 2,187 and 3,097 were Bostrichidae, accounting for 37% and 66% in KU and Mitaboni, respectively. A total of 12 bostrichid species was identified, including Sinoxylon ruficorne, S. doliolum, Xylion adustus, Xyloperthodes nitidipennis, Xyloperthella picea, Xylopsocus castanoptera, Lyctus brunneus, Heterbostrychus brunneus, Xylopsocus sp., and Dinoderus gabonicus. The most abundant species in KU was Xylion adustus with 1,915 beetles accounting for 88.4%, and Sinoxylon ruficorne in Mitaboni with 1,050 beetles accounting for 33.9% of the total. Sinoxylon ruficorne was only recorded in Mitaboni while only 2 specimens of D. gabonicus were found in KU. The mean number of exit holes on A. xanthophloea differed significantly between sites, which corresponded approximately to the amount of economic damage caused by the beetles to the structural integrity of the lumber. In addition, a number of predators in the family Cerambycidae, Cleridae, Histeridae and parasitoids from Braconidae, Ichneumonidae, and Chalcididae were recovered, suggesting a need to conduct further studies to document these species' diversity, parasitism rates and efficacy for possible biological control.

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Project description:The SARS-CoV-2 P.1 lineage emerged in Amazonas (AM), North Brazil and its evolution has been dynamically reported associated with increased transmissibility and/or immune evasion. Here, we evaluated the lineages circulating in 29 cities in Rio Grande do Sul (RS), Southern Brazil between March 2020 and May 2021 and investigated the genetic events associated with the emergence of the P.1. A total of 202 oro/nasopharyngeal SARS-CoV-2 specimens from patients during routine hospital care were submitted to whole-genome sequencing. Phylogenetic and Bayesian Evolutionary Analyses of the P.1 lineage were carried out to determine the relationship between sequences from RS and AM and dated their common ancestor and origin. One hundred six (53%) sequences were assigned as P.1 and most carried the 22 lineage-defining mutations. All the P.1 sequences included other important mutations, such as P314L and R203K/G204R, and revealed a high genetic diversity in the phylogenetic tree. The time-scaled inference suggests that the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM, but the origin of some sequences from RS is unknown. Further, the common ancestor of sequences from RS is dated to mid-June/July 2020, earlier than those previously reported from AM. Our results demonstrate that there is a high degree of genetic diversity among P.1 sequences, which suggests a continuous evolution and community spread of the virus. Although the first P.1 outbreak was reported in AM, the lineage was associated with multiple introductory events and had already been circulating in Southern Brazil prior to November 2020. IMPORTANCE The SARS-CoV-2 P.1 lineage is associated with increased transmissibility and/or immune evasion and presents a dynamic evolution in Brazil. The significance of our research relies in the fact that we evaluated the SARS-CoV-2 lineages circulating in Southern Brazil between March 2020 and May 2021. This evaluation allowed us to detect the genetic events associated with the emergence of the P.1 and its sublineages. This study is important because we were able to establish that the common ancestor of P.1 sequences from Rio Grande do Sul, Southern Brazil, is dated of mid-June/July 2020, earlier than the P.1 sequences previously reported from Amazonas (AM) state. Noteworthy, the high degree of genetic diversity among P.1 sequences found in this study suggests a continuous evolution and community spread of the virus. Moreover, the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM.

Project description:SARS-CoV-2 caused a life-threatening COVID-19 pandemic outbreak worldwide. The Southeastern Region of Wisconsin, USA (SERW) includes large urban Milwaukee and six suburban counties, namely Kenosha, Ozaukee, Racine, Walworth, Washington and Waukesha. Due to the lack of detailed SARS-CoV-2 genomic surveillance in the suburban populations of the SERW, whole-genome sequencing was employed to investigate circulating SARS-CoV-2 lineages and characterize dominant XBB lineages among this SERW population from November 2021 to April 2023. For an unbiased data analysis, we combined our 6709 SARS-CoV-2 sequences with 1520 sequences from the same geographical region submitted by other laboratories. Our study shows that SARS-CoV-2 genomes were distributed into 357 lineages/sublineages belonging to 13 clades, of which 88.8% were from Omicron. We document dominant sublineages XBB.1.5 and surging XBB.1.16 and XBB.1.9.1 with a few additional functional mutations in Spike, which are known to contribute to higher viral reproduction, enhanced transmission and immune evasion. Mutational profile assessment of XBB.1.5 Spike identifies 38 defining mutations with high prevalence occurring in 49.8-99.6% of the sequences studied, of which 32 mutations were in three functional domains. Phylogenetic and genetic relatedness between XBB.1.5 sequences reveal potential virus transmission occurring within households and within and between Southeastern Wisconsin counties. A comprehensive phylogeny of XBB.1.5 with global sub-dataset sequences confirms the wide spread of genetically similar SARS-CoV-2 strains within the same geographical area. Altogether, this study identified proportions of circulating Omicron variants and genetic characterization of XBB.1.5 in the SERW population, which helped state and national public health agencies to make compelling mitigation efforts to reduce COVID-19 transmission in the communities and monitor emerging lineages for their impact on diagnostics, treatments and vaccines.

Dataset Information

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

Publications

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

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