Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

BackgroundUsing classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. MethodsSARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens. ResultsOver the pandemic duration (March 2020 - January 2022) Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%), and Omicron (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country. ConclusionsThe emergence of Alpha, Delta, and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.

BSL-3 Laboratory User Training Program at NUITM-KEMRI

Pathogens handled in a Biosafety Level 3 (BSL-3) containment laboratory pose significant risks to laboratory staff and the environment. It is therefore necessary to develop competency and proficiency among laboratory workers and to promote appropriate behavior and practices that enhance safety through biosafety training. Following the installation of our BSL-3 laboratory at the Center for Microbiology Research-Kenya Medical Research Institute in 2006, a biosafety training program was developed to provide training on BSL-3 safety practices and procedures. The training program was developed based on World Health Organization specifications, with adjustments to fit our research activities and biosafety needs. The program is composed of three phases, namely initial assessment, a training phase including theory and a practicum, and a final assessment. This article reports the content of our training program.

BSL-3 Laboratory User Training Program at NUITM-KEMRI

Pathogens handled in a Biosafety Level 3 (BSL-3) containment laboratory pose significant risks to laboratory staff and the environment. It is therefore necessary to develop competency and proficiency among laboratory workers, and promote behaviors and practices that enhance safety through biosafety training. Following installation of our BSL-3 laboratory at the Center for Microbiology Research-Kenya Medical Research Institute, in 2006, a biosafety training program was developed to provide training on BSL-3 safety practices and procedures. The training program was developed based on the World Health Organization specifications, with adjustments to fit our research activities and biosafety needs. The program is composed of three phases namely; initial assessment, a training phase that includes theory and practicum, and final assessment. This article reports the content of our training program.

Infectra(®)-kit: a device for restraining mice and confining tsetse flies during trypanosome infection transmission experiments.

Chemical (anaesthesia) and manual techniques are commonly used to restrain mice during vector-mediated parasite transmission experiments in the laboratory. Chemical restraint may interfere with natural fly vector-mouse interactions and therefore potentially affect the outcome of transmission experiments. Conversely, manual restraint is labour-intensive and exposes laboratory animals to excessive restraining-related discomfort. We report development of a mouse restraining device (Infectra(®)-kit) that allows essential transmission studies to be carried out with minimal human manipulation and without the need for anaesthesia. Infectra(®)-kit can be used as a single unit for restraining one mouse or as eight-assembled units, thus significantly improving efficiency of a single operator in comparison to manual restraint. The kit was validated by comparing feeding success in tsetse flies fed on mice restrained using Infectra(®)-kit (Group I) to those manually restrained (Group II). The mean±SE % feeding success was 75.0±8.2% and 82.1±8.2% for tsetse flies in Groups I and II respectively. Statistical analysis using two sample t-test showed no significant difference between the two groups at p≤0.05, indicating that Infectra(®)-kit as a restraining device was as good as the conventional manual restraint method. The main benefits of using Infectra(®)-kit for transmission studies therefore include reduction of man-hours and animal restraining-related discomfort. In addition, the risk of accidental injury to laboratory personnel by either mice or tsetse flies is minimized, which is an important consideration when working with zoonotic parasites.