A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations, predominantly from Europe, which diminished following the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1 and C.1.1. Although distorted by low sampling numbers and blind-spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.

Status of insecticide resistance in malaria vectors in Kwale County, Coastal Kenya.

BACKGROUND: The strategy for malaria vector control in the context of reducing malaria morbidity and mortality has been the scale-up of long-lasting insecticidal nets to universal coverage and indoor residual spraying. This has led to significant decline in malaria transmission. However, these vector control strategies rely on insecticides which are threatened by insecticide resistance. In this study the status of pyrethroid resistance in malaria vectors and it's implication in malaria transmission at the Kenyan Coast was investigated. RESULTS: Using World Health Organization diagnostic bioassay, levels of phenotypic resistance to permethrin and deltamethrin was determined. Anopheles arabiensis showed high resistance to pyrethroids while Anopheles gambiae sensu stricto (s.s.) and Anopheles funestus showed low resistance and susceptibility, respectively. Anopheles gambiae sensu lato (s.l.) mosquitoes were further genotyped for L1014S and L1014F kdr mutation by real time PCR. An allele frequency of 1.33% for L1014S with no L1014F was detected. To evaluate the implication of pyrethroid resistance on malaria transmission, Plasmodium falciparum infection rates in field collected adult mosquitoes was determined using enzyme linked immunosorbent assay and further, the behaviour of the vectors was assessed by comparing indoor and outdoor proportions of mosquitoes collected. Sporozoite infection rate was observed at 4.94 and 2.60% in An. funestus s.l. and An. gambiae s.l., respectively. A higher density of malaria vectors was collected outdoor and this also corresponded with high Plasmodium infection rates outdoor. CONCLUSIONS: This study showed phenotypic resistance to pyrethroids and low frequency of L1014S kdr mutation in An. gambiae s.l. The occurrence of phenotypic resistance with low levels of kdr frequencies highlights the need to investigate other mechanisms of resistance. Despite being susceptible to pyrethroids An. funestus s.l. could be driving malaria infections in the area.

Status of insecticide susceptibility in Anopheles gambiae sensu lato and Anopheles funestus mosquitoes from western Kenya.

The status of resistance was investigated in Anopheles gambiae sensu lato and An. funestus (Diptera: Culicidae) mosquitoes from western Kenya to four classes of insecticides approved by World Health Organization for indoor residual spraying. The prevalence of the knockdown-resistance (kdr) mutation associated with resistance to pyrethroids and DDT was determined in An. gambiae s.l.. Standard World Health Organization diagnostic bioassay kits for DDT (an organochlorine), fenitrothion (an organophosphate), bendiocarb (a carbamate), and the pyrethoirds, lambdacyhalothrin and permethrin, were used. Knockdown every 10 min and mortality 24 h after exposure were noted. Controls not treated with insecticides and with the susceptible An. gambiae KISUMU strain were included in the bioassays. The presence of the kdr gene was determined using a standard diagnostic polymerase chain reaction assay. Over 98% mortality was observed for tests with all insecticides for both An. gambiae s.l. and An. funestus. Knockdown rates were not significantly different between An. gambiae s.l. and the KISUMU strain control. 50% and 95% knockdown times were either slightly lower than those for the KISUMU strain or higher by factors of less than 1.6. The mean frequency of the East African kdr mutation was 24.7% in An. gambiae sensu strictu. Based on conventional criteria where susceptibility is defined by mortality rates >98% 24 h after exposure, no evidence for resistance was found, implying that vector control measures employing any of the insecticides tested would be unhampered by resistance. The observed frequencies of the kdr mutation do not appear to compromise the effectiveness of the insecticides. The need for continuous monitoring of the status of insecticide resistance and of the impact of any observed resistance on the efficacy of vector control programs employing insecticides is apparent.