Shehu Shagari Awandu

Malaria remains a significant global health challenge with 263 million cases in 2023. Anopheles insecticide resistance threatens current vector control methods, and novel strategies are crucial to combat malaria transmission. Wolbachia , an endosymbiotic bacteria that can invade mosquito populations and inhibit pathogen replication, has only recently been shown as a high‐density symbiont in two wild Anopheles species. Detection of Wolbachia in symbiosis with Anopheles mosquitoes has relied on PCR amplification of Wolbachia genes and/or Sanger and Illumina sequencing. This study assesses Oxford Nanopore Technology (ONT) to detect Wolbachia , which could facilitate screening for symbiosis with wild Anopheles mosquitoes in endemic settings. We used 46 samples; 10 were pooled for a single MinION flow cell run and the rest processed individually using Flongle flow cells, comparing three mosquito species with three kit combinations. Using the ONT Field sequencing kit, there were 13X more Wolbachia reads in An. demeilloni (genuine symbiosis) than An. gambiae (no evidence of Wolbachia ). The ONT 16S barcoding kit and Rapid barcoding kit were then assessed using more economical Flongle flow cells. Wolbachia was successfully identified in An . demeilloni and An. moucheti but not in An. gambiae . This study demonstrates the feasibility of ONT for field‐based detection of Wolbachia .

Malaria, a mosquito-borne disease predominantly affecting sub-Saharan Africa, remains a significant global health challenge with 263 million cases in 2023. Although progress in vaccine development has recently occurred, insecticide resistance has reduced the effectiveness of the main stay method of traditional vector control and novel innovative vector control strategies against Anopheles mosquitoes is crucial to combat the spread of malaria. Wolbachia is an endosymbiotic bacterium that can invade mosquito populations and inhibit human pathogens. Historically Wolbachia was thought to not occur naturally within wild Anopheles An .) populations, but recent evidence has confirmed the presence of at least two strains in genuine symbiosis. Detection of Wolbachia strains has pre-dominantly relied on PCR amplification of Wolbachia genes and/or sanger and illumina sequencing. In this study, we assess the use of Oxford Nanopore Technology (ONT) for detecting bacteria within wild Anopheles mosquitoes and determine the ability to detect the endosymbiotc bacterium Wolbachia . We assessed Wolbachia detection from library preparations using the ONT Field sequencing kit for MinION sequencing on the Mk1C and found a pool size of 10 mosquitoes is required preventing individual mosquito analysis. There were roughly 13 times more Wolbachia reads in pooled Anopheles demeilloni compared to An. gambiae . Utilizing the more economical Flongle flow cells and Mk1B device, we further evaluated the effectiveness of two library preparation methods that are compatible: Rapid PCR Barcoding and 16S Barcoding kits. Our findings indicate that the 16S Barcoding Kit in conjunction with the Flongle flowcell effectively identified Wolbachia in both Anopheles demeilloni and Anopheles moucheti but we found no evidence of Wolbachia in Anopheles gambiae . Our study demonstrates the feasibility of developing ONT for field-based sequencing in malaria-endemic regions, providing a potentially lower cost and ‘field friendly’ method for monitoring mosquito populations and associated endosymbionts. Graphical

Background Persistent human papillomavirus (HPV) infection is considered the primary etiological factor for invasive cervical cancer. Understanding the epidemiology of circulating potential high-risk (HR) and HR HPV strains is essential in updating epidemiological knowledge and recommendations on genotype-specific vaccination development. In Lake Victoria Basin-LVB (Kisumu and Siaya Counties, Kenya), both the HIV burden, the post-COVID-19 pandemic environment and the population growth point to the need to study the current circulating strains. This study determined the prevalence and factors associated with Potential HR/HR HPV among women attending selected reproductive health clinics in LVB. The prevalence of Potential HR/HR HPV, genotype-specific distributions, and implications to the current HPV vaccination ongoing within Kenya are discussed. Methods A cross-sectional facility-based survey made up of 434 women aged 16-68 years was carried out in two selected facilities in the Urban-Kisumu County (Jaramogi Oginga Odinga Teaching and Referral Hospital-[JOOTRH] and rural-Siaya County (Gobei Health Center). Structured questionnaires were conducted to collect participant clinical and social characteristics. Cervical specimens were collected by registered reproductive health nurses and HPV genotyping was carried out using RIATOL HPV genotyping qPCR assay. Descriptive statistics followed by logistic binary regression was done using R version 4.3.2 Results The overall prevalence of potential HR/HR HPV among women attending the selected reproductive health clinics was reported at 36.5% (158/434). Specifically, in the rural setting, Gobei Health Center, the prevalence was 41.4% (41/99) while in the urban setting-JOOTRH, it was 34.6% (117/335). The most prevalent potential HR/HR HPV are 52, 67, 16, 31, 39, 45, and 31 for both HIV-positive and negative women and either in rural-Gobei Health Centre and Urban-JOOTRH. In this study, HIV status was not associated with potential HR/HR HPV among women attending. Age was the main factor associated with HPV infection among HIV-positive and negative women attending the selected reproductive health clinics in rural-urban Lake Victoria Basin, with women between the age of 30-39 having the highest risk (AOR=0.3, CI:0.2-0.7, p<0.001). Conclusion In both rural and urban regions, potential HR/HR HPV infection among individuals attending reproductive health clinics at the selected facilities remains common. The study identifies the need for effective implementation and clinical follow-up process of cervical cancer control program in the Lake Victoria Basin.

Background: Various milestones have been set targeting the elimination of schistosomiasis with the vision of “a world free of schistosomiasis” including the 2020 and 2025 goals. Despite the increased control and prevention efforts, schistosomiasis still affects many people, partly because treatment doesn’t cover all at-risk populations. Preventive chemotherapy (PC), the cornerstone of control interventions is primarily inclined toward school-age children (SAC), whose prevalence also informs interventions for other age groups in the community. Whereas prevalence in SAC has been shown to be a good indicator of the prevalence in other age groups, it remains to be seen as if this is not true in different epidemiological settings and risk areas. Methods: This study evaluated the predictive value of schistosomiasis prevalence among SAC in estimating community-wide prevalence in Siaya County, Kenya. A single stool sample was collected from participants aged 2-50 years. Stool samples were collected from preschool-age children (2-6 years), SAC (7-14 years), adolescents (15 to 0 to S. mansoni . There was no significant difference between the mean egg intensity of S. mansoni in SAC compared to the other age groups. There was a strong positive correlation between SAC prevalence and intensity and community-wide prevalence and intensity; r _s =0.8, Ps =0.6, PS. mansoni prevalence and S. mansoni prevalence in SAC was observed. The regression analysis indicated that SAC prevalence/intensity can be used to predict overall S. mansoni prevalence/intensity. In terms of age groups, it can predict in all age groups but adolescents. Conclusions: In this setting, generally, the prevalence of S. mansoni among SAC was a good predictor of the prevalence in other age groups and the overall (all age groups combined) prevalence. However, in terms of risk strata SAC data was only a good predictor of overall prevalence and intensity only in the moderate risk stratum. These findings suggest that S. mansoni prevalence and intensity among SAC are valid for community sampling purposes and informing interventions including MDA at the community level.

Background Physically disabled persons continue to face discrimination, exclusion and neglect which hamper equitable access to services and disproportionately affect them during a pandemic. This study aimed to evaluate the physical access barriers to COVID-19 vaccines among persons with physical disabilities during the COVID-19 pandemic, (March, 2020 to March, 2022) in Ugenya Subcounty, Siaya County in western Kenya. Methods The study design was cross sectional involving physically disabled persons. A simple random sampling technique was used to recruit participants 108 participants. Structured questionnaires were used to collect data needed. Results Marital status, (χ² = 13.310, p = 0.004), mobility impairment, (χ² ₌ 16.168, p = 0.001), source of information, (χ² = 4.022, p = 0.002), vaccination site, (χ² = 95.480, p =0.001), motivation, (χ² ₌ 95.457, p = 0.045), decision time, (χ² = 95.501, p = 0.001) and access to room, (χ² = 84.098, p = 0.001), all had statistically significant associations with access to and uptake of COVID-19 vaccines. Multinomial logistic regression analysis showed that fare used and age, (0.001), alongside transport means and age, (p = 0.004), had statistically significant associations with COVID-19 vaccine access and uptake. Those who had difficulty both in movement and speaking found it hard to access and receive COVID-19 vaccines, (p = 0.001). Conclusion Marital status, information from reliable sources, belief in existence of COVID-19 were associated with access to and uptake of COVID-19 vaccines. Additionally, nonpayment of transport fare increased the odds of being vaccinated. Therefore, programs such as mobile health teams or reimbursement of fare should be adopted to increase access to healthcare by the physically disabled.

Background: Epstein Barr virus (EBV)-associated endemic Burkitt’s Lymphoma pediatric cancer is associated with morbidity and mortality among children resident in holoendemic Plasmodium falciparum regions in western Kenya. P. falciparum exerts strong selection pressure on sickle cell trait (SCT), alpha thalassemia (-α^3.7/αα), glucose-6-phosphate dehydrogenase (G6PD), and merozoite surface protein 2 (MSP-2) variants (FC27, 3D7) that confer reduced malarial disease severity. The current study tested the hypothesis that SCT, (-α^3.7/αα), G6PD mutation and (MSP-2) variants (FC27, 3D7) are associated with an early age of EBV acquisition. Methods: Data on infant EBV infection status (< 6 and ≥ 6–12 months of age) was abstracted from a previous longitudinal study. Archived infant DNA (n = 81) and mothers DNA (n = 70) samples were used for genotyping hemoglobinopathies and MSP-2. The presence of MSP-2 genotypes in maternal DNA samples was used to indicate infant in-utero malarial exposure. Genetic variants were determined by TaqMan assays or standard PCR. Group differences were determined by Chi-square or Fisher’s analysis. Bivariate regression modeling was used to determine the relationship between the carriage of genetic variants and EBV acquisition. Results: EBV acquisition for infants < 6 months was not associated with -α^3.7/αα (OR = 1.824, P = 0.354), SCT (OR = 0.897, P = 0.881), or G6PD [Viangchan (871G > A)/Chinese (1024 C > T) (OR = 2.614, P = 0.212)] and [Union (1360 C > T)/Kaiping (1388G > A) (OR = 0.321, P = 0.295)]. There was no relationship between EBV acquisition and in-utero exposure to either FC27 (OR = 0.922, P = 0.914) or 3D7 (OR = 0.933, P = 0.921). In addition, EBV acquisition in infants ≥ 6–12 months also showed no association with -α^3.7/αα (OR = 0.681, P = 0.442), SCT (OR = 0.513, P = 0.305), G6PD [(Viangchan (871G > A)/Chinese (1024 C > T) (OR = 0.640, P = 0.677)], [Mahidol (487G > A)/Coimbra (592 C > T) (OR = 0.948, P = 0.940)], [(Union (1360 C > T)/Kaiping (1388G > A) (OR = 1.221, P = 0.768)], African A (OR = 0.278, P = 0.257)], or in utero exposure to either FC27 (OR = 0.780, P = 0.662) or 3D7 (OR = 0.549, P = 0.241). Conclusion: Although hemoglobinopathies (-α^3.7/αα, SCT, and G6PD mutations) and in-utero exposure to MSP-2 were not associated with EBV acquisition in infants 0–12 months, novel G6PD variants were discovered in the population from western Kenya. To establish that the known and novel hemoglobinopathies, and in utero MSP-2 exposure do not confer susceptibility to EBV, future studies with larger sample sizes from multiple sites adopting genome-wide analysis are required.

The population’s antibody response is a key factor in comprehending SARS-CoV-2 epidemiology. This is especially important in African settings where COVID-19 impact, and vaccination rates are relatively low. This study aimed at characterizing the Immunoglobulin G (IgG) and Immunoglobulin M (IgM) in both SARS-CoV-2 asymptomatic and symptomatic individuals in Kisumu and Siaya counties in western Kenya using enzyme linked immunosorbent assays. The IgG and IgM overall seroprevalence in 98 symptomatic and asymptomatic individuals in western Kenya between December 2021-March 2022 was 76.5% (95% CI = 66.9–84.5) and 29.6% (95% CI = 20.8–39.7) respectively. In terms of gender, males had slightly higher IgG positivity 87.5% (35/40) than females 68.9% (40/58). Amidst the ongoing vaccination roll-out during the study period, over half of the study participants (55.1%, 95% CI = 44.7–65.2) had not received any vaccine. About one third, (31.6%, 95% CI = 22.6–41.8) of the study participants had been fully vaccinated, with close to a quarter (13.3% 95% CI = 7.26–21.6) partially vaccinated. When considering the vaccination status and seroprevalence, out of the 31 fully vaccinated individuals, IgG seropositivity was 81.1% (95% CI = 70.2–96.3) and IgM seropositivity was 35.5% (95% CI = 19.22–54.6). Out of the participants that had not been vaccinated at all, IgG seroprevalence was 70.4% (95% CI 56.4–82.0) with 20.4% (95% CI 10.6–33.5) seropositivity for IgM antibodies. On PCR testing, 33.7% were positive, with 66.3% negative. The 32 positive individuals included 12(37.5%) fully vaccinated, 8(25%) partially vaccinated and 12(37.5%) unvaccinated. SARs-CoV-2 PCR positivity did not significantly predict IgG (p = 0.469 [95% CI 0.514–4.230]) and IgM (p = 0.964 [95% CI 0.380–2.516]) positivity. These data indicate a high seroprevalence of antibodies to SARS-CoV-2 in western Kenya. This suggests that a larger fraction of the population was infected with SARS-CoV-2 within the defined period than what PCR testing could cover.

Coronavirus is a disease caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged as a global pandemic in 2019 from Wuhan, China. Since its emergence, it has caused immense suffering to human life, 6.27 million lives have been lost, movement curtailed and social dynamics disrupted. The golden standard for getting samples for SARS-CoV-2 detection is through oral- nasopharyngeal swab, this method of sample collection is invasive and uncomfortable, thus stigmatized the general population, and thereby impeded the progress of controlling the spread through mass testing. Being a contact disease, mechanisms to encourage mass testing is key to reduce the spread. This study thus developed a complimentary sample type to test for SARS-CoV-2, the use of human feces. Fecal samples were collected from 100 asym-symptomatic individuals suspected to be infected with COVID-19, virus RNA was then extracted and profiled through Real Time Polymerase Chain Reaction (RT-qPCR). The antigen rapid diagnostic test revealed high positivity rate of 44%, but the real time polymerase chain reaction results on nasopharyngeal and fecal samples revealed a significant variation, high number of the patients tested positive with stool samples compared to the nasopharyngeal swabs, with 43 and 37%, respectively. SARS-CoV-2 virus was detected in both symptomatic and asymptomatic individuals; however, the symptomatic registered a higher positivity of 25% compared to 20% among the asymptomatic patients. Vaccination only lowered the risk of infection, fully and partially vaccinated lowered the infection level to 10% compared to 20% among the unvaccinated. Finally, gender parity in relation to COVID19 was evaluated, more females (56%) compared to males were recruited in this study, out of which (20; 43.4%) were positive, and 26 (56.6%) were negative based on fecal RT-qPCR outcomes. Based on the outcome of this study, rapid diagnostic test (Ag-RDT) however cheap and or fast does not provide accurate information, moreover, the virus does not stay longer within the Oro-nasopharyngeal region, thus the invalid or negative results, thus use of feces should be adopted as a confirmatory test to ascertain the COVID19 status of an individual.

Background The population’s antibody response is a key factor in comprehending SARS-CoV-2 epidemiology. This is especially important in African settings where COVID-19 impact, and vaccination rates are relatively low. This study aimed at characterizing the Immunoglobulin G (IgG) and Immunoglobulin M (IgM) in both SARS-CoV-2 asymptomatic and symptomatic individuals in Kisumu and Siaya counties in Western Kenya using enzyme linked immunosorbent assays. Results The IgG and IgM overall seroprevalence in 98 symptomatic and asymptomatic individuals in western Kenya between December 2021-March 2022 was 76.5% (95% CI =66.9-84.5) and 31.6% (95% CI =22.6-41.8) respectively. In terms of gender, males had slightly higher IgG positivity 87.8% (36/41) than females 68.4% (39/57). Amidst the ongoing vaccination roll-out during the study period, over half of the study participants (55.1%, 95% CI= 44.7-65.2) had not received any vaccine. About one third, (30.6%, 95% CI= 21.7-40.7) of the study participants had been fully vaccinated, with close to a quarter (14.3% 95% CI=8.04-22.8) partially vaccinated. When considering the vaccination status and seroprevalence, out of the 30 fully vaccinated individuals, IgG seropositivity was 86.7% (95% CI =69.3-96.2) and IgM seropositivity was 40% (95% CI =22.7-59.4). Out of the participants that had not been vaccinated at all, IgG seroprevalence was 70.3% (95% CI 56.4-82.0) with 20.4% (95% CI 10.6-33.5) seropositivity of IgM antibodies. SARs-CoV-2 PCR positivity did not significantly predict IgG (p = 0.457 [95% CI 0.514-4.371]) and IgM (p = 0.858 [95% CI 0.350-2.395]) positivity. Conclusion Our data indicate a high seroprevalence of antibodies to SARS-CoV-2 in western Kenya. This suggests larger fraction of the population were infected with SARS-CoV-2 within the defined period than what PCR testing could cover.

We longitudinally assessed P. falciparum parasite kinetics, gametocyte production and infectivity in incident infections that were naturally acquired following infection clearance and in chronic asymptomatic infections in Burkina Faso. 92% (44/48) of the incident cohort developed symptoms and were treated within 35 days, compared to 23% (14/60) of the chronic cohort. All but two individuals with chronic infection were gametocytaemic at enrollment, whereas only 35% (17/48) in the incident cohort developed gametocytes within 35 days. The relative abundance of ap2-g transcripts was positively associated with conversion to gametocyte production (i.e. the ratio of gametocytes at day 14 to ring stage parasites at baseline) and was higher in chronic infections. Parasite multiplication rate, assessed by daily molecular parasite quantification, was positively associated with prospective gametocyte production. Most incident infections were cleared before gametocyte density was sufficiently high to infect mosquitoes. In contrast, chronic, asymptomatic infections represented a significant source of mosquito infections. If present, gametocytes were significantly less infectious if concurrent with malaria symptoms. Our observations support the notion that malaria transmission reduction may be expediated by enhanced case management, involving both symptom-screening and infection detection.