Comparative analysis of SARS-CoV-2 detection methods using stool, blood, and nasopharyngeal swab samples.

Introduction: as a public health policy, the ongoing global coronavirus disease 2019 vaccination drives require continuous tracking, tracing, and testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnostic testing is important in virus detection and understanding its spread for timely intervention. This is especially important for low-income settings where the majority of the population remains untested. This is well supported by the fact that of about 9% of the Kenyan population had been tested for the virus. Methods: this was a cross-sectional study conducted at the Kisumu and Siaya Referral Hospitals in Kenya. Here we report on the sensitivity and specificity of the rapid antigen detection test (Ag-RDT) of SARS-CoV-2 compared with the quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) using stool and nasopharyngeal swab samples. Further, the mean Immunoglobulin M (IgM) and Immunoglobulin G (IgG) antibody levels among symptomatic and asymptomatic individuals in western Kenya were evaluated. Results: the sensitivity and specificity of Ag-RDT were 76.3% (95% CI, 59.8-88.6%) and 96.3% (95% CI, 87.3-99.5%) with a negative and positive predictive value of 85% (95% CI, 73.8%-93.0%) and 93% (95% CI, 78.6%-99.2%) respectively. There was substantial agreement of 88% (Kappa value of 0.75, 95% CI, 0.74-0.77) between Ag-RDT and nasopharyngeal swab RT-qPCR, and between stool and nasopharyngeal swab RT-qPCR results (83.7% agreement, Kapa value 0.62, 95% CI 0.45-0.80). The mean IgM and IgG antibody response to SARS-CoV-2 were not different in asymptomatic individuals, 1.11 (95% CI, 0.78-1.44) and 0.88 (95% CI, 0.65-1.11) compared to symptomatic individuals 4.30 (95% CI 3.30-5.31) and 4.16 (95% CI 3.32 -5.00). Conclusion: the choice of an appropriate SARS-CoV-2 diagnostic, screening, and surveillance test should be guided by the specific study needs and a rational approach for optimal results.

Contribution of pollution gradient to the sediment microbiome and potential pathogens in urban streams draining into Lake Victoria (Kenya).

In sub-Saharan Africa (SSA), urban rivers/streams have long been subjected to anthropogenic pollution caused by urbanization, resulting in significantly altered chemical and biological properties of surface water and sediments. However, little is known about the diversity and structure of river microbial community composition and pathogens, as well as how they respond to anthropogenic inputs. High-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used in this study to conduct a comprehensive analysis of the spatial bacterial distribution and metabolic functions in sediment of two urban streams (Kisat and Auji) flowing through Kisumu City, Kenya. Results revealed that sediment samples from the highly urbanized mid and lower stream catchment zones of both streams had significantly higher levels of total organic carbon (TOC), total nitrogen (TN), total phosphorous (TP) than the less urbanized upper catchment zone, and were severely polluted with toxic heavy metals lead (Pb), cadmium (Cd), and copper (Cu). Differential distribution of Actinobacteria, Proteobacteria, Chloroflexi, and Verrucomicrobia in sediment bacterial composition was detected along stream catchment zones. The polluted mid and lower catchment zones were rich in Actinobacteria and Proteobacteria, as well as a variety of potential pathogenic taxa such as Corynebacterium, Staphylococcus, Cutibacterium, Turicella, Acinetobacter, and Micrococcus, as well as enteric bacteria such as Faecalibacterium, Shewanella, Escherichia, Klebsiella, Enterococcus, Prevotella, Legionella, Vibrio and Salmonella. Furthermore, PICRUSt metabolic inference analysis revealed an increasing enrichment in the sediments of genes associated with carbon and nitrogen metabolism, disease pathogenesis, and virulence. Environmental factors (TOC, Pb, Cd, TN, pH) and geographical distance as significant drivers of sediment bacterial community assembly, with the environmental selection to play a dominant role. In polluted river catchment zone sediment samples, Pb content was the most influential sediment property, followed by TOC and Cd content. Given the predicted increase in urbanization in SSA, further alteration of surface water and sediment microbiome due to urban river pollution is unavoidable, with potential long-term effects on ecosystem function and potential health hazards. As a result, this study provides valuable information for ecological risk assessment and management of urban rivers impacted by diffuse and point source anthropogenic inputs, which is critical for future proactive and sustainable urban waste management, monitoring, and water pollution control in low-income countries.

High seroprevalence of Immunoglobulin G (IgG) and IgM antibodies to SARS-CoV-2 in asymptomatic and symptomatic individuals amidst vaccination roll-out in western Kenya.

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.