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.

Malaria and COVID-19, though caused by different organisms, share a significant number of symptoms like fever, headaches, difficulty in breathing and fatigue. Therefore, determining if a patient is positive for COVID-19 or Malaria based on symptoms alone, might be misleading, especially during pandemic response. It has been reported that an individual begins to manifest Malaria symptoms between 10 -15 days after infection with malaria parasite, although some individuals may be asymptomatic. Some COVID-19 infected patients, like Malaria, are also asymptomatic but could contribute to transmission of SARS-CoV-2 virus. These similarities in symptoms have led to misconception about COVID-19 being real and misdiagnoses of both infections, especially in Nigeria. However, there are possibilities that Malaria and COVID-19 could co-exist in some individuals thereby leading to mismanagement and treatment of only one infection while neglecting the possibility of the patient being infected with both diseases. We aim to determine possible correlation between Malaria and COVID-19 in a Malaria endemic country like Nigeria. This study was carried out using the qPCR molecular testing approach, a gold standard for COVID-19 testing and rapid diagnostic test kits to detect Malaria parasites in 617 individuals residing in urban settings. We demonstrated that COVID-19 and Malaria infection amongst adults in urban settings are unrelated thereby focusing on symptoms alone may result in misdiagnosis. Our findings show that Malaria

In an outbreak, effective detection of the aetiological agent(s) involved using molecular techniques is key to efficient diagnosis, early prevention and management of the spread. However, sequencing is necessary for mutation monitoring and tracking of clusters of transmission, development of diagnostics and for vaccines and drug development. Many sequencing methods are fast evolving to reduce test turn-around-time and to increase through-put compared to Sanger sequencing method; however, Sanger sequencing remains the gold standard for clinical research sequencing with its 99.99% accuracy This study sought to generate sequence data of SARS-CoV-2 using Sanger sequencing method and to characterize them for possible site(s) of mutations. About 30 pairs of primers were designed, synthesized, and optimized using endpoint PCR to generate amplicons for the full length of the virus. Cycle sequencing using BigDye Terminator v.3.1 and capillary gel electrophoresis on ABI 3130xl genetic analyser were performed according to the manufacturers’ instructions. The sequence data generated were assembled and analysed for variations using DNASTAR Lasergene 17 SeqMan Ultra. Total length of 29,760bp of SARS-CoV-2 was assembled from the sample analysed and deposited in GenBank with accession number: MT576584. Blast result of the sequence assembly shows a 99.97% identity with the reference sequence. Variations were noticed at positions: nt201, nt2997, nt14368, nt16535, nt20334, and nt28841-28843, which caused amino acid alterations at the S (aa614) and N (aa203-204) regions. The mutations observed at S and N-gene in this study may be indicative of a gradual changes in the genetic coding of the virus hence, the need for active surveillance of the viral genome.

IssuesQuality-management systems (QMS) are uncommon in clinical laboratories in Nigeria, and until recently, none of the nation’s 5 349 clinical laboratories have been able to attain the certifications necessary to begin the process of attaining international accreditation. Nigeria’s Human Virology Laboratory (HVL), however, began implementation of a QMS in 2006, and in 2008 it was determined that the laboratory conformed to the requirements of ISO 9001:2000 (now 2008), making it the first diagnostic laboratory to be certified in Nigeria. The HVL has now applied for the World Health Organization (WHO) accreditation preparedness scheme. The experience of the QMS implementation process and the lessons learned therein are shared here.DescriptionIn 2005, two personnel from the HVL spent time studying quality systems in a certified clinical laboratory in Dakar, Senegal. Following this peer-to-peer technical assistance, several training sessions were undertaken by HVL staff, a baseline assessment was conducted, and processes were established. The HVL has monitored its quality indicators and conducted internal and external audits; these analyses (from 2007 to 2009) are presented herein.Lessons learnedAlthough there was improvement in the pre-analytical and analytical indicators analysed and although data-entry errors decreased in the post-analytical process, the delay in returning laboratory test results increased significantly. There were several factors identified as causes for this delay and all of these have now been addressed except for an identified need for automation of some high-volume assays (currently being negotiated). Internal and external audits showed a trend of increasing non-conformities which could be the result of personnel simply becoming lax over time. Application for laboratory accreditation, however, could provide the renewed vigour needed to correct these non-conformities.RecommendationThis experience shows that sustainability of the QMS at present is a cause for concern. However, the tiered system of accreditation being developed by WHO–Afro may act as a driving force to preserve the spirit of continual improvement.

Introduction: effective and safe means of sample collection is a crucial component of testing for Covid-19. Uptake of testing is key to containing and controlling the spread of the virus. Scientists have been working on various strategies that will increase the uptake of testing for COVID-19. One such method involves the use of the drive-through sampling strategy. Methods: data was collected by both qualitative and quantitative methods. An eligibility form was filled online. While in-depth interviews were conducted for the qualitative aspect of the study. Results: 2,600 visits were recorded at the website, 2300 (88.46%) participants successfully registered for the test. 57.4% were found eligible of which 78.0% presented for the test. This Consisted of 78.0% drive-through and 22.0% walk-in. The average time for transiting through the drive-through site was 19.2 ± 4.6minutes while that of the walk-in was 28 ± 9.2min. This difference was statistically significant (p<0.001). In the qualitative component, respondents opined that maximum safety measures were deployed to protect both participants and health workers. Most said that the turnaround time for the sampling process was short. Conclusion: the sampling strategy although largely successful, is largely dependent on Internet penetrability, thus this sampling modality will be best utilized as an adjunct to established models of sample collection.