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

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.

Development and Pilot Testing of a Context-Relevant Safe Anesthesia Checklist for Cesarean Delivery in East Africa.

BACKGROUND: Maternal mortality rate in developing countries is 20 times higher than in developed countries. Detailed reports surrounding maternal deaths have noted an association between substandard management during emergency events and death. In parallel with these findings, there is increasing evidence for cognitive aids as a means to prevent errors during perioperative crises. However, previously published findings are not directly applicable to cesarean delivery in low-income settings. Our hypothesis was that the use of obstetric anesthesia checklists in the management of high-fidelity simulated obstetrical emergency scenarios would improve adherence to best practice guidelines in low- and middle-income countries. METHODS: Accordingly, with input from East African health care professionals, we created a context-relevant obstetric anesthesia checklist for cesarean delivery. Second, clinical observations were performed to assess in a real-world setting. Third, a pilot testing of the cognitive aid was undertaken. RESULTS: Clinical observation data highlighted significant deficiencies in the management of obstetric emergencies. The use of the cesarean delivery checklist during simulations of peripartum hemorrhage and preeclampsia showed significant improvement in the percentage of completed actions (pretraining 23% ± 6% for preeclampsia and 22% ± 13% for peripartum hemorrhage, posttraining 75% ± 9% for preeclampsia, and 69% ± 9% for peripartum hemorrhage [P < .0001, both scenarios; data as mean ± standard deviation]). CONCLUSIONS: We developed, evaluated, and begun implementation of a context-relevant checklist for the management of obstetric crisis in low- and middle-income countries. We demonstrated not only the need for this tool in a real-world setting but also confirmed its potential efficacy through a pilot simulation study.

Monitoring Anesthesia Care Delivery and Perioperative Mortality in Kenya Utilizing a Provider-driven Novel Data Collection Tool.

BACKGROUND: Perioperative mortality rate is regarded as a credible quality and safety indicator of perioperative care, but its documentation in low- and middle-income countries is poor. We developed and tested an electronic, provider report-driven method in an East African country. METHODS: We deployed a data collection tool in a Kenyan tertiary referral hospital that collects case-specific perioperative data, with asynchronous automatic transmission to central servers. Cases not captured by the tool (nonobserved) were collected manually for the last two quarters of the data collection period. We created logistic regression models to analyze the impact of procedure type on mortality. RESULTS: Between January 2014 and September 2015, 8,419 cases out of 11,875 were captured. Quarterly data capture rates ranged from 423 (26%) to 1,663 (93%) in the last quarter. There were 93 deaths (1.53%) reported at 7 days. Compared with four deaths (0.53%) in cesarean delivery, general surgery (n = 42 [3.65%]; odds ratio = 15.80 [95% CI, 5.20 to 48.10]; P < 0.001), neurosurgery (n = 19 [2.41%]; odds ratio = 14.08 [95% CI, 4.12 to 48.10]; P < 0.001), and emergency surgery (n = 25 [3.63%]; odds ratio = 4.40 [95% CI, 2.46 to 7.86]; P < 0.001) carried higher risks of mortality. The nonobserved group did not differ from electronically captured cases in 7-day mortality (n = 1 [0.23%] vs. n = 16 [0.58%]; odds ratio =3.95 [95% CI, 0.41 to 38.20]; P = 0.24). CONCLUSIONS: We created a simple solution for high-volume, prospective electronic collection of perioperative data in a lower- to middle-income setting. We successfully used the tool to collect a large repository of cases from a single center in Kenya and observed mortality rate differences between surgery types.

A sample-to-answer COVID-19 diagnostic device based on immiscible filtration and CRISPR-Cas12a-assisted detection.

In response to the ongoing coronavirus disease 2019 (COVID-19) pandemic and disparities of vaccination coverage in low-and middle-income countries, it is vital to adopt a widespread testing and screening programme, combined with contact tracing, to monitor and effectively control the infection dispersion in areas where medical resources are limited. This work presents a lab-on-a-chip device, namely 'IFAST-LAMP-CRISPR', as an affordable, rapid and high-precision molecular diagnostic means for detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The herein proposed 'sample-to-answer' platform integrates RNA extraction, amplification and molecular detection with lateral flow readout in one device. The microscale dimensions of the device containing immiscible liquids, coupled with the use of silica paramagnetic beads and guanidine hydrochloride, streamline sample preparation (including RNA extraction, concentration and purification) in 15 min with minimal hands-on steps. The pre-amplification in combination with CRISPR-Cas12a detection assays targeting the nucleoprotein (N) gene achieved visual identification of ≥ 470 copies mL-1 genomic SARS-CoV-2 samples in 45 min. On-chip assays showed the ability to isolate and detect SARS-CoV-2 RNA from 100 genome copies mL-1 of replication-deficient viral particles in 1 h. This simple, affordable and integrated platform demonstrated a visual, faster, and yet specificity- and sensitivity-comparable alternative to the costly gold-standard reverse transcription-polymerase chain reaction (RT-PCR) assay, requiring only a simple heating source. Initial testing illustrates the platform viability both on nasopharyngeal swab and saliva samples collected using the easily accessible Swan-brand cigarette filter, providing a complete workflow for COVID-19 diagnostics in low-resource settings.

Assessing malaria burden during pregnancy in Mali.

Malaria infection during pregnancy is associated with adverse consequences including low birth weight (LBW) and maternal anemia, particularly in primigravidae and secundigravidae. In preparation for a clinical trial of the efficacy of chloroquine (CQ) and sulfadoxine-pyrimethamine (SP) containing prevention regimens during pregnancy, we conducted a one-year cross sectional study in Koro and Bandiagara, Mali using an assessment methodology developed by the Centers for Disease Control and Prevention (CDC) to generate basic data on malarial burden during pregnancy. Two hundred and sixty-one and 192 women were enrolled in Koro and Bandiagara, respectively. Rates of placental parasitemia were 17.1 and 42.3% in Koro and Bandiagara, respectively, despite high (70-80%) use of preventive medication (mainly CQ). Low gravidity (1st and 2nd pregnancies) was associated with peripheral (p<0.001) and placental (p<0.001) malaria only in Bandiagara, whereas it was associated with low birth weight in both sites (p<0.001 in Koro and p=0.002 in Bandiagara). First and second pregnancies were the most important characteristics associated with placental malaria (RR=2.78, 95%CI 1.81-4.29) and (ARR=2.06, 95%CI 1.03-4.15) and low birth weight (RR=4.26, 95%CI 2.50-7.27) and (ARR=4.51, 95%CI 2.55-8.00). Birth during the rainy season was associated with placental infection in univariate analysis. Characteristics such as younger age, having fever during pregnancy, and unmarried status were associated with low birth weight only in univariate analysis and singleton premature delivery and low gravidity were associated with low birth weight in both univariate and multivariate analysis. Data from this assessment demonstrated the high burden of malaria during pregnancy in Mali. Results had been used by researchers as local reference data and by ministry of health for to stop recommending CQ prophylaxis. The methodology could be used by other malaria-endemic countries to direct their national malaria program efforts.

Comparison of intermittent preventive treatment with chemoprophylaxis for the prevention of malaria during pregnancy in Mali.

BACKGROUND: Malaria during pregnancy contributes to maternal anemia and low birth weight. In East Africa, several studies have demonstrated that intermittent preventive treatment (IPT) with sulfadoxine-pyrimethamine (SP) is more efficacious than weekly chloroquine (CQ) chemoprophylaxis in preventing these adverse consequences. To our knowledge, there are no published trials evaluating IPT in West Africa. METHODS: We undertook a randomized controlled trial of weekly CQ chemoprophylaxis, 2-dose IPT with CQ, and 2-dose IPT with SP; 1163 women were enrolled. RESULTS: In multivariate analyses, when compared with weekly CQ, IPT/SP was associated with a reduction in third-trimester anemia (adjusted odds ratio [AOR], 0.49; P<.001), placental parasitemia (AOR, 0.69; P=.04), and low birth weight (<2500 g) (AOR, 0.69; P=.04). The prevalence of placental infection remained unexpectedly high, even in the IPT/SP group (24.5%), possibly because of the intensity of seasonal transmission. There were no significant differences in stillbirths, spontaneous abortions, or neonatal deaths among the 3 groups. CONCLUSIONS: In Mali, IPT with SP appears more efficacious than weekly chloroquine chemoprophylaxis in preventing malaria during pregnancy. These data support World Health Organization recommendations to administer at least 2 doses of IPT during pregnancy. In intensely seasonal transmission settings in Mali, >2 doses may be required to prevent placental reinfection prior to delivery.