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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.

There is a need for reliable serological assays to determine accurate estimates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence. Most single target antigen assays have shown some limitations in Africa. To assess the performance of a multi-antigen assay, we evaluated a commercially available SARS-CoV-2 Multi-Antigen IgG assay for human coronavirus disease 2019 (COVID-19) in Nigeria. Validation of the xMAP SARS-CoV-2 Multi-Antigen IgG assay was carried out using well-characterized SARS-CoV-2 reverse transcription polymerase chain reactive positive (97) and pre-COVID-19 pandemic (86) plasma panels. Cross-reactivity was assessed using pre-COVID-19 pandemic plasma specimens (213) from the 2018 Nigeria HIV/AIDS Indicator and Impact Survey (NAIIS). The overall sensitivity of the xMAP SARS-CoV-2 Multi-Antigen IgG assay was 75.3% [95% CI: 65.8%- 82.8%] and specificity was 99.0% [95% CI: 96.8%- 99.7%]. The sensitivity estimate increased to 83.3% [95% CI: 70.4%- 91.3%] for specimens >14 days post-confirmation of diagnosis. However, using the NAIIS pre-pandemic specimens, the false positivity rate was 1.4% (3/213). Our results showed overall lower sensitivity and a comparable specificity with the manufacturer's validation. There appears to be less cross-reactivity with NAIIS pre-pandemic COVID-19 specimens using the xMAP SARS-CoV-2 Multi-Antigen IgG assay. In-country SARS-CoV-2 serology assay validation can help guide the best choice of assays in Africa.

A key element in containing the spread of the SARS-CoV-2 infection is quality diagnostics which is affected by several factors. We now report the comparative performance of five real-time diagnostic assays. Nasopharyngeal swab samples were obtained from persons seeking a diagnosis for SARS-CoV-2 infection in Lagos, Nigeria. The comparison was performed on the same negative, low, and high-positive sample set, with viral RNA extracted using the Qiagen Viral RNA Kit. All five assays are one-step reverse transcriptase real-time PCR assays. Testing was done according to each assay’s manufacturer instructions for use using real-time PCR platforms. 63 samples were tested using the five qPCR assays, comprising of 15 negative samples, 15 positive samples (Ct = 16–30; one Ct = 35), and 33 samples with Tib MolBiol E-gene Ct value ranging from 36–41. All assays detected all high positive samples correctly. Three assays correctly identified all negative samples while two assays each failed to correctly identify one different negative sample. The consistent detection of positive samples at different Ct/Cq values gives an indication of when to repeat testing and/or establish more stringent in-house cut-off value. The varied performance of different diagnostic assays, mostly with emergency use approvals, for a novel virus is expected. Comparative assays’ performance reported may guide laboratories to determine both their repeat testing Ct/Cq range and/or cut-off value.

The 2022 multi-country mpox (formerly monkeypox) outbreak, driven by mpox virus (MPXV) Clade IIb poses renewed threat to global public health. The cessation of smallpox vaccination has created large immunologically naïve cohorts, with uncertain implications for contemporary MPXV susceptibility. To assess whether residual vaccination-derived immunity influences exposure risk, we combine serological and phylodynamic analyses. Using a six-plex Luminex assay, we measure immunoglobulin G (IgG) binding to six MPXV antigens in 176 Nigerian adults comprising of 75 healthcare workers sampled in 2021 and 101 community volunteers sampled in 2023. At baseline, 24/176 (13.6%) were MPXV seropositive, predominantly born before 1980. Magnitude-breadth analysis scores were two-fold higher in pre-1980 cohort relative to post-1980 cohort. In 153 participants with follow-up samples (median 9 months), 5/153 (3%) showed evidence of exposure, with ≥2-fold increases in magnitude-breadth scores and antigen-specific responses against ≥4/6 antigens without reported clinical illness. Antigen-specific responses were strongest to B6R (11-fold), followed by M1R and A35R, with marked individual-level heterogeneity. Complementary phylodynamic reconstruction of 105 Nigerian MPXV genomes identified sporadic transmission against frequent dead-end infections. Together, these data show that residual smallpox immunity continues to shape mpox transmission and asymptomatic exposure contributes to under-detected spread, informing surveillance and targeted vaccination strategies. There are limited data on mpox immunity in West Africa. In this study, authors present serological and genomic evidence of residual smallpox vaccination immunity and possibly unrecognized mpox exposure among ostensibly healthy Nigerian adults.

Population-based study is known to be a very essential type of study during and after a pandemic or epidemic, as it provides crucial information on the incidence, prevalence, and risk factors of the disease in question. There has been limited information about the challenges faced in conducting such surveys in Nigeria. In this paper, we will share our experience, and describe the challenges faced in conducting a population-based seroepidemiological study of COVID–19 in Lagos, Nigeria. Some challenges were peculiar to specific Local Government Areas (LGAs) while others were general. The challenges include general misconceptions of community members about health research, difficulties in mapping houses, planning for data collection, standardizing data collection, working in hard-to-reach communities when resources were limited as well as difficulty in collection of blood and naso-oropharyngeal swabs. Ways of overcoming these problems, lessons learnt, and recommendations are hereby discussed.

Background The COVID-19 pandemic posed a major public health challenge with varying devastating effects on the global community. Vaccination is the most effective measure in combating this pandemic. A major challenge, especially in resource-limited settings, was the shortage of the vaccines. However, evidence by WHO in the use of fractionated doses in combating yellow fever prompted the evaluation of the safety and immunogenicity of fractionated doses of COVID-19 vaccines (ChAd0x1, AD26.COV2.S, and BNT162B2) among Nigerian adults (18–65 years). Methods This is a multi-center, non-inferiority randomized, triple-blind trial involving 1812 COVID-19 vaccine naïve participants. Six hundred four eligible participants will be randomized into each of the three vaccine arms of ChAd0x1, AD26.COV2.S, and BNT162B2 COVID-19 vaccine. 151 participants will be randomized each into the 25% and 50% fractionated dose and 300 in the standard full dose arm for the ChAd0x1 and AD26.COV2.S group. In the BNT162B2 group, 201 participants will be randomized into the 50% fractionated dose and 403 into the standard dose arms. The efficacy (immunogenicity) will be evaluated by collecting blood samples at baseline (day 0) and day 28 after immunization to determine the geometric mean fold rise (GMFR) of ≥ 2.5 within the range of 20% non-inferiority to the standard dose of anti-SARS-CoV-2 S antibody response detected by ELISA termed as seroconversion. Safety and adverse events will be evaluated through active evaluation during the first 72 h of vaccine administration and on days 14 and 28 of clinic visits. The trial will also assess secondary immunogenicity variables of 50% plaque plaalite reduction neutralization by antibodies against SARS-CoV-2 variants (α, δ, and κ) and cytokines production (IFNα, γ, and IL-2 producing CD4 and CD8 T lymphocytes). Discussion The proposed trial will allow for a comprehensive understanding of the immunologic responses and safety profile of fractional doses compared to full doses of COVID-19 vaccines among Nigerian adults. In addition, this will guide policy implementation for prompt vaccination of the population to maximize access to the limited vaccines available during the COVID-19 pandemic or future epidemics/pandemics. Trial registration The study is registered at the Pan African Clinical Trials Registry (PACTR), a primary registry in the WHO International Clinical Trial Platforms. PACTR202206754734018. Registered on June 1, 2022, Accessible at: https://pactr.samrc.ac.za/ Trial Sponsor: Open Philanthropy.

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.

The first case of COVID-19 in Nigeria was recorded on February 27, 2020, being an imported case by an Italian expatriate, to the country. Since then, there has been steady increase in the number of cases. However, the number of cases in Nigeria is low in comparison to cases reported by other countries with similar large populations, despite the poor health system prevailing in the country. This has been mainly attributed to the low testing capacity in Nigeria among other factors. Therefore, there is a need for innovative ways to increase the number of persons testing for COVID-19. The aim of the study was to pilot a nasopharyngeal swab self-sample collection model that would help increase COVID-19 testing while ensuring minimal person-to-person contact being experienced at the testing center. 216 participants took part in this study which was carried out at the Nigerian Institute of Medical Research between June and July 2020. Amongst the 216 participants, 174 tested negatives for both self-collected samples and samples collected by Professionals, 30 tested positive for both arms, with discrepancies occurring in 6 samples where the self-collected samples were positive while the ones collected by the professionals were negative. The same occurred in another set of 6 samples with the self-collected samples being negative and the professional—collected sample coming out positive, with a sensitivity of 83.3% and a specificity of 96.7%. The results of the interrater analysis are Kappa = 0.800 (95% CI, 0.690 to 0.910) which implies an outstanding agreement between the two COVID-19 sampling methods. Furthermore, since p< 0.001 Kappa (k) coefficient is statistically different from zero, our findings have shown that self-collected samples can be reliable in the diagnosis of COVID-19.

Background Two vaccines, the JYNNEOS and ACAM 2000 have been approved for use for Mpox protection, however vaccine hesitancy and vaccine refusal poses a significant challenge in its uptake. This study explored participants’ awareness of Mpox, willingness, and barriers to receiving the approved Mpox vaccines when they become available in Nigeria. Method This was a qualitative cross-sectional study. Participants were recruited using a purposive sampling technique. A total of 16 Focus Group Discussions (FGDs) and 64 in-depth interviews (IDIs) were conducted by trained research assistants among community members in four states in Nigeria (Bayelsa, Delta, Lagos, and Rivers states) between October 1 and November 30, 2023. The interviews were audio-recorded and transcribed before thematic analysis was conducted. Results One hundred and sixty-four persons, comprising 71 males and 93 females, participated in this study. The anticipated rollout of the Mpox vaccine in Nigeria elicited mixed reactions; while some participants expressed willingness to be vaccinated, others expressed their concerns about the vaccine side effects, vaccine safety, and their mistrust of new vaccines. There were also reports about physical access and financial cost being a barrier to receiving the Mpox vaccine. Conclusion The study highlights the critical need for more community-based public health education campaigns to enhance awareness and correct misconceptions about Mpox. Effective communication strategies that address specific community issues and emphasize vaccine safety are important for increasing vaccination uptake and controlling the spread of Mpox in Nigeria.

Healthcare workers (HCWs) are disproportionately infected with SARS-CoV-2 when compared to members of the general public; estimating the seroprevalence of SARS-CoV-2 antibody and SARS-CoV-2 infection rate among HCWs is therefore crucial. This study was carried out in four health facilities in Lagos Nigeria to determine the prevalence of IgG antibodies (seroprevalence) and SARS-CoV-2 active infection rate via a positive rtPCR result, the cross-sectional study was conducted between December 2020 and July 2021. Nasopharyngeal and blood samples were collected from HCWs and screened for SARS-CoV-2 infection using the rtPCR technique and antibody using the Abbott anti-SARS-CoV-2 IgG CMIA assay, respectively. Demographic and occupational exposures data were obtained and analysed using descriptive and inferential statistics, variables significant via inferential statistics were subjected to a multivariate analysis. A total of 413 participants were enrolled, with a mean age in years of 38.4±11.0. The seroprevalence was 30.9% (115/372) while 63/395 (15.9%) were actively infected with the virus. HCWs whose job role had direct contact with patients had a higher percentage of SARS-CoV-2 infection when compared with those not in direct contact, also being a health care worker was significantly associated with getting a positive COVID-19 PCR result. In conclusion the SARS-CoV-2 seroprevalence seen in this study was higher than national serosurvey estimates indicating HCWs are at higher risk of COVID-19 infection when compared to the general public. Vaccination and effective implementation of infection control measures are important to protect HCWs.