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.

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

Background: The global COVID-19 outbreak relies on a quantitative real-time polymerase chain reaction (qRT-PCR) for the detection of severe acute respiratory syndrome coronavirus (SARS-CoV-2), to facilitate the 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 our setting, where the supply of testing reagents is limited. Methods: Standards generated from a serially-diluted positive control and previously identified positive/negative samples were used to determine the optimal volumes of the qRT-PCR reagents and to evaluate the validity and performance of four assays: Charité Berlin and European Virus Archive - GLOBAL (EVAg) primer-probe sets, and DAAN and Beijing Genomics Institute (BGI) premixed commercial kits. A multiplex and singleplex RT-PCR kit was used with the two primer-probe sets and the recommended assay volumes of the two premixed kits were altered. Results: In comparison to the multiplex RT-PCR kit, the singleplex RT-PCR kit combined with the primer-probe sets yielded consistent cycle threshold (Ct) values across the different titrations tested. The DAAN premixed kit produced comparable Ct values across the titrations, while the BGI kit showed incomparable Ct values and inconsistent results between batches using the manufacturer's recommended volumes. Conclusion: We achieved a 2.5-fold and 4-fold increase in the number of tests/kit for the premixed kits and the primer-probe sets, respectively. The primer-probe set assays were reliable and consistent, and we preferred a combination of an EVAg and a Berlin target. Any inconclusive result was repeated by different individuals following the same protocol. DAAN was a consistent and reliable assay even at lower concentrations from the stated recommendations. BGI in contrast, required dilution to improve its performance and was hence an assay that was used in combination with EVAg or Berlin targets.

External built residential environment characteristics that affect mental health of adults

External built residential environment characteristics include aspects of building design such as types of walls, doors and windows, green spaces, density of houses per unit area, and waste disposal facilities. Neighborhoods that are characterized by poor quality external built environment can contribute to psychosocial stress and increase the likelihood of mental health disorders. This study investigated the relationship between characteristics of external built residential environment and mental health disorders in selected residences of Nakuru Municipality, Kenya. External built residential environment characteristics were investigated for 544 residents living in different residential areas that were categorized by their socioeconomic status. Medically validated interview schedules were used to determine mental health of residents in the respective neighborhoods. The relationship between characteristics of the external built residential environment and mental health of residents was determined by multivariable logistic regression analyses and chi-square tests. The results show that walling materials used on buildings, density of dwelling units, state of street lighting, types of doors, states of roofs, and states of windows are some built external residential environment characteristics that affect mental health of adult males and females. Urban residential areas that are characterized by poor quality external built environment substantially expose the population to daily stressors and inconveniences that increase the likelihood of developing mental health disorders.

An evaluation of clinical indicators for severe paediatric illness

To help reduce paediatric morbidity and mortality in the developing world, WHO has developed a diagnostic and treatment algorithm that targets the principal causes of death in children, which include acute respiratory infection, malaria, measles, diarrhoeal disease, and malnutrition. With this algorithm, known as the Sick Child Charts, severely ill children are rapidly identified, through the presence of any one of 13 signs indicative of severe illness, and referred for more intensive health care. These signs are the inability to drink, abnormal mental status (abnormally sleepy), convulsions, wasting, oedema, chest wall retraction, stridor, abnormal skin turgor, repeated vomiting, stiff neck, tender swelling behind the ear, pallor of the conjunctiva, and corneal ulceration. The usefulness of these signs, both in current clinical practice and within the optimized context of the Sick Child Chart algorithm in a rural district of western Kenya, was evaluated. We found that 27% of children seen in outpatient clinics had one or more of these signs and that pallor and chest wall retraction were the signs most likely to be associated with hospital admission (odds ratio (OR) = 8.6 and 5.3, respectively). Presentation with any of these signs led to a 3.2 times increased likelihood of admission, although 54% of hospitalized children had no such signs and 21% of children sent home from the outpatient clinic had at least one sign. Among inpatients, 58% of all children and 89% of children who died had been admitted with a sign. Abnormal mental status was the sign most highly associated with death (OR = 59.6), followed by poor skin turgor (OR = 5.6), pallor (OR = 4.3), repeated vomiting (OR = 3.6), chest wall retraction (OR = 2.7), and oedema (OR = 2.4). Overall, the mortality risk associated with having at least one sign was 6.5 times higher than that for children without any sign. While these signs are useful in identifying a subset of children at high risk of death, their validation in other settings is needed. The training and supervision of health workers to identify severely ill children should continue to be given high priority because of the benefits, such as reduction of childhood mortality.