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

No abstract

BackgroundMonitoring mosquito population dynamics is essential to guide selection and evaluation of malaria vector control interventions but is typically implemented by mobile, centrally-managed teams who can only visit a limited number of locations frequently enough to capture longitudinal trends. Community-based (CB) mosquito trapping schemes for parallel, continuous monitoring of multiple locations are therefore required that are practical, affordable, effective, and reliable.MethodsA CB surveillance scheme, with a monthly sampling and reporting cycle for capturing malaria vectors, using Centers for Disease Control and Prevention light traps (LT) and Ifakara Tent Traps (ITT), were conducted by trained community health workers (CHW) in 14 clusters of households immediately surrounding health facilities in rural south-east Zambia. At the end of the study, a controlled quality assurance (QA) survey was conducted by a centrally supervised expert team using human landing catch (HLC), LT and ITT to evaluate accuracy of the CB trapping data. Active surveillance of malaria parasite infection rates amongst humans was conducted by CHWs in the same clusters to determine the epidemiological relevance of these CB entomological surveys.ResultsCB-LT and CB-ITT exhibited relative sampling efficiencies of 50 and 7%, respectively, compared with QA surveys using the same traps. However, cost per sampling night was lowest for CB-LT ($13.6), followed closely by CB-ITT ($18.0), both of which were far less expensive than any QA survey (HLC: $138, LT: $289, ITT: $269). Cost per specimen of Anopheles funestus captured was lowest for CB-LT ($5.3), followed by potentially hazardous QA-HLC ($10.5) and then CB-ITT ($28.0), all of which were far more cost-effective than QA-LT ($141) and QA-ITT ($168). Time-trends of malaria diagnostic positivity (DP) followed those of An. funestus density with a one-month lag and the wide range of mean DP across clusters was closely associated with mean densities of An. funestus caught by CB-LT (P < 0.001).ConclusionsCB trapping schemes appear to be far more affordable, epidemiologically relevant and cost-effective than centrally supervised trapping schemes and may well be applicable to enhance intervention trials and even enable routine programmatic monitoring of vector population dynamics on unprecedented national scales.

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

BackgroundLong-lasting, insecticidal nets (LLINs) and indoor residual spraying (IRS) are the most widely accepted and applied malaria vector control methods. However, evidence that incremental impact is achieved when they are combined remains limited and inconsistent.MethodsFourteen population clusters of approximately 1000 residents each in Zambia’s Luangwa and Nyimba districts, which had high pre-existing usage rates (81.7 %) of pyrethroid-impregnated LLINs were quasi-randomly assigned to receive IRS with either of two pyrethroids, namely deltamethrin [Wetable granules (WG)] and lambdacyhalothrin [capsule suspension (CS)], with an emulsifiable concentrate (EC) or CS formulation of the organophosphate pirimiphos methyl (PM), or with no supplementary vector control measure. Diagnostic positivity of patients tested for malaria by community health workers in these clusters was surveyed longitudinally over pre- and post-treatment periods spanning 29 months, over which the treatments were allocated and re-allocated in advance of three sequential rainy seasons.ResultsSupplementation of LLINs with PM CS offered the greatest initial level of protection against malaria in the first 3 months of application (incremental protective efficacy (IPE) [95 % confidence interval (CI)] = 0.63 [CI 0.57, 0.69], P < 0.001), followed by lambdacyhalothrin (IPE [95 % CI] = 0.31 [0.10, 0.47], P = 0.006) and PM EC (IPE, 0.23 [CI 0.15, 0.31], P < 0.001) and then by deltamethrin (IPE [95 % CI] = 0.19 [−0.01, 0.35], P = 0.064). Neither pyrethroid formulation provided protection beyond 3 months after spraying, but the protection provided by both PM formulations persisted undiminished for longer periods: 6 months for CS and 12 months for EC. The CS formulation of PM provided greater protection than the combined pyrethroid IRS formulations throughout its effective life IPE [95 % CI] = 0.79 [0.75, 0.83] over 6 months. The EC formulation of PM provided incremental protection for the first 3 months (IPE [95 % CI] = 0.23 [0.15, 0.31]) that was approximately equivalent to the two pyrethroid formulations (lambdacyhalothrin, IPE [95 % CI] = 0.31 [0.10, 0.47] and deltamethrin, IPE [95 % CI] = 0.19 [−0.01, 0.35]) but the additional protection provided by the former, apparently lasted an entire year.ConclusionWhere universal coverage targets for LLIN utilization has been achieved, supplementing LLINs with IRS using pyrethroids may reduce malaria transmission below levels achieved by LLIN use alone, even in settings where pyrethroid resistance occurs in the vector population. However, far greater reduction of transmission can be achieved under such conditions by supplementing LLINs with IRS using non-pyrethroid insecticide classes, such as organophosphates, so this is a viable approach to mitigating and managing pyrethroid resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12936-016-1143-7) contains supplementary material, which is available to authorized users.