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.

Zika virus (ZIKV) is one of the arboviruses implicated in febrile illness, microcephaly and other neurological disorders in babies whose mothers were infected during pregnancy. Information on ZIKV in Nigeria is limited. Hence, this study was aimed at investigating the seroprevalence of Zika virus among pregnant women in Lagos State. In a cross-sectional study, blood samples collected from 352 randomly selected pregnant women in four hospitals in Lagos State were separated and plasma analyzed using Zika virus IgG and IgM capture Enzyme-linked immunosorbent assay (Demeditec Diagnostics, Germany). The optical densities were read using Precision Microplate reader (Molecular devices) and cut-off calculated according to manufacturer’s guide. Parameters and symptoms such as history of fever, rashes on the body, exposure to mosquito were extracted from the questionnaire and analyzed. IgM seropositive samples were screened for ZIKV RNA on RT-qPCR. Out of 352 samples screened, 7(2.0%) and 5(1.4%) of the pregnant women tested positive for IgG and IgM respectively. None tested positive for both IgG and IgM markers. Statistical analysis showed that there is no significant relationship between the symptoms analyzed in this study at 95% Confidence interval except conjunctivitis. None of the ZIKV IgM seropositive samples tested positive for ZIKV RNA on RT-qPCR. The results show that there is evidence of exposure to Zika virus among the population studied in Lagos, Nigeria. Also, the low level seroprevalence of the virus in the population studied indicates that there is lack of herd immunity of Zika virus infection in Lagos, Nigeria.

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