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

Intrinsic and extrinsic factors associated with sputum characteristics of presumed tuberculosis patients.

BACKGROUND:Sputum remains the most preferred specimen for detection of Mycobacterium tuberculosis due to its non-invasive method of production. Good quality sputum specimen is essential for accurate diagnosis of pulmonary tuberculosis (PTB). It is therefore imperative to assess factors that are related to the production of sputum that is of the best quality. OBJECTIVE:We assessed the intrinsic and extrinsic characteristics of presumed tuberculosis patients and the quality of sputum they produced. METHODS:This was a cross-sectional study in which consenting enrolled presumed tuberculosis patients were subjected to medical examination and a structured questionnaire administered to collect clinical history, demographic information, environmental and behavioral characteristics. The enrolled participants were instructed on how to collect spot and morning sputum specimens for macroscopic and microscopic assessment to determine any association. RESULTS:A total of 309 patients were enrolled into the study with an even distribution on gender (50.5% males). Of these, 202 (65.3%) submitted both a spot and a morning specimen for analysis. On macroscopic examination, 70% spot and 68% morning sputum were characterized as good quality (Purulent/mucoid). The factors associated (p<0.05) with quality specimen included both intrinsic and extrinsic factors. The intrinsic factors included: difficulty in breathing, presence of conjunctivitis and knowledge of the disease whereas the only extrinsic factor associated with production of good quality sputum for tuberculosis diagnosis was time taken by patient to seek tuberculosis treatment after occurrence of any of the TB symptoms. CONCLUSION:Both intrinsic and extrinsic factors affected the quality of sputum produced by presumed tuberculosis patients. Clinical and behavioral characteristics including conjunctivitis, difficulty in breathing and delay in seeking treatment were important factors that determined the production of good quality sputum specimens, while knowledge of tuberculosis disease did not compel presumed tuberculosis patients to produce good quality sputum for diagnosis of the disease

An optimization of four SARS-CoV-2 qRT-PCR assays in a Kenyan laboratory to support the national COVID-19 rapid response teams

Background: The COVID-19 pandemic relies on real-time polymerase chain reaction (qRT-PCR) for the detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to facilitate roll-out of patient care and infection control measures. There are several qRT-PCR assays with little evidence on their comparability. We report alterations to the developers’ recommendations to sustain the testing capability in a resource-limited setting. Methods: We used a SARS-CoV-2 positive control RNA sample to generate several 10-fold dilution series that were used for optimization and comparison of the performance of the four qRT-PCR assays: i) Charité Berlin primer-probe set, ii) European Virus Archive – GLOBAL (EVAg) primer-probe set, iii) DAAN premixed commercial kit and iv) Beijing Genomics Institute (BGI) premixed commercial kit. We adjusted the manufacturer- and protocol-recommended reaction component volumes for these assays and assessed the impact on cycle threshold (Ct) values. Results: The Berlin and EVAg E gene and RdRp assays reported mean Ct values within range of each other across the different titrations and with less than 5% difference. The DAAN premixed kit produced comparable Ct values across the titrations, while the BGI kit improved in performance following a reduction of the reaction components. Conclusion: We achieved a 2.6-fold and 4-fold increase in the number of tests per kit for the commercial kits and the primer-probe sets, respectively. All the assays had optimal performance when the primers and probes were used at 0.375X, except for the Berlin N gene assay. The DAAN kit was a reliable assay for primary screening of SARS-CoV-2 whereas the BGI kit’s performance was dependent on the volumes and concentrations of both the reaction buffer and enzyme mix. Our recommendation for SARS-CoV-2 diagnostic testing in resource-limited settings is to optimize the assays available to establish the lowest volume and suitable concentration of reagents required to produce valid results