Search

Population-based study is known to be a very essential type of study during and after a pandemic or epidemics, as it provides important information on the incidence, prevalence and risk factors of the disease in question. There has been limited information about challenges faced in conducting such surveys in Nigeria. In this paper, we would share our experience, and describe the challenges faced in conducting 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 misconception of community members about health research, difficulties in mapping houses, planning for data collection, standardising data collection, working in hard-to-reach community when resources were limited as well as difficulty in collection of blood, oral and naso-oropharyngeal swabs. Ways of overcoming these problems, lessons learnt, and recommendations are hereby discussed.

Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the B.1.1.318 and B.1.525 variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Our results show how regional connectivity in downsampled regions like Africa can often influence virus transmissions between neighbouring countries. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission in the region, generating actionable information for public health decision makers in the region.

BackgroundAccess to vaccines has contributed to the control of COVID-19. However, evaluation of the effectiveness of the vaccines in a setting where the vaccines were not originally tested is critically important. This study evaluates the clinical and laboratory characteristics of COVID-19 vaccine breakthrough infections among healthcare workers (HCWs).MethodsA multicentre prospective study among HCWs who had two doses of the Oxford/AstraZeneca ChAdOx1-S [recombinant] (AZD1222) vaccine were followed up 24 weeks. Nasopharyngeal and oropharyngeal specimens were tested using RT-PCR for SARS-CoV-2 and positive samples were subjected to whole genome sequencing for variant assignment.ResultA total of 369 HCWs were enrolled; of which 24 (6.5%) had breakthrough infections. There was equal sex distribution among the breakthrough cases. The majority were aged between 30 to 39years (37.5%), and had mild symptoms of cough, fever, headache, and nausea/vomiting (58%), with no hospitalization. Among the 24 breakthrough cases whose whole genomes were successfully sequenced, three were confirmed to be Delta B.1.617.2 variant during the 3rdwave and an additional three were confirmed as omicron B.1.1.529 variant during the 4thwave.ConclusionWe reported vaccine breakthrough cases among fully vaccinated HCWs with the majority presenting with mild illness. Both delta and omicron variants were identified during the different epidemiologic spectrums of SARS-CoV-2. Therefore, there is a need to scale up vaccination for all front-line health workers and high-risk populations in developing countries.

BackgroundThere are no real world data on vaccine elicited neutralising antibody responses for the world’s most widely used vaccine, AZD1222, in African populations following scale up. Here, we measured i) baseline SARS-CoV-2 seroprevalence and levels of protective neutralizing antibodies prior to vaccination rollout using both flow cytometric based analysis of binding antibodies to nucleocapsid (N), coupled with virus neutralisation approaches and ii) neutralizing antibody responses to VOC prior to vaccination (January 2021) and after two-doses of AZD1222 vaccine administered with a 12 week interval in Lagos, Nigeria - a period when the Delta variant was circulating.MethodsHealth workers at multiple sites in Lagos were recruited to the study. For binding antibody measurement, IgG antibodies against SARS-COV-2 Wuhan-1 receptor-binding domain (RBD), trimeric spike protein (S), nucleocapsid protein (N) and Omicron S1 were measured using the Luminex-based SARS-CoV-2-IgG assay by flow cytometry. For plasma neutralising antibody measurement, SARS-CoV-2 lentiviral pseudovirus (PV) were prepared by transfecting 293T cells with Wuhan-614G wild type (WT), B.1.617.2 (Delta) and BA.1 (Omicron) plasmids in conjunction with HIV-1 expression vectors and luciferase encoding genome flanked by LTRs. We performed serial plasma dilutions from each time point and mixed plasma with PV before infecting HeLa-ACE2 cell lines, reading out luminescence and calculating ID50 (reciprocal dilution of sera required to inhibit 50% of PV infection).ResultsOur underlying study population receiving at least one dose of vaccine comprised 140 participants with a median age of 40 (interquartile range: 33, 48). 62/140 (44%) participants were anti-N IgG positive prior to administration of first vaccine dose. 49 had plasma samples available at baseline prior to vaccination and at two follow-up timepoints post two dose vaccination for neutralization assays. Half of the participants, 25/49 (51%) were IgG anti-N positive at baseline. Of the 24 individuals anti-N Ab negative at baseline, 12/24 had ID50 above the cut-off of 20. In these individuals, binding antibodies to S were also detectable, and neutralisation correlated with IgG anti-S, suggesting waning of N antibody after infection. Overall, neutralizing Ab titres to WT 1 month after second dose were 2579 and at 3 months post second-dose were 1695. As expected, lower levels of neutralization were observed against the Delta GMT 549 and Omicron variants 269 at 1 month. Positive anti-N IgG Ab status at baseline was associated with significantly higher titres of neutralizing antibodies following vaccination across all tested VOC. Those with anti-N Abs present at baseline did not experience waning of responses between months 1 and 3 post second dose. When data were analysed for negative anti-N IgG status at any timepoint, there was a significant decline in neutralization and binding antibodies between 1 month and 3 months post second-dose. The GMT in these individuals for Delta and Omicron was approximately 100, nearly a log lower in comparison to WT. We tested anti-N IgG in subjects who were anti-N IgG negative at baseline (n=78) and became positive between 1- and 3-months post second dose and found 7/49 (14%) with de-novo infection, with one additional participant demonstrating both reinfection and breakthrough infection to yield a total breakthrough rate of 8/49 (16%). Neutralising and binding Ab titres 1 month post vaccine, prior to breakthrough, were not associated with breakthrough infection. Neutralizing titres were higher at the last time point in individuals who had experienced vaccine breakthrough infection (with no evidence of infection prior to vaccine), indicating a boosting effect of infection in addition to vaccine. However, neutralisation and binding S antibodies against Omicron were low in those with either prior exposure or infection following two dose AZD1222.ConclusionsAZD1222 is immunogenic in this real world west African cohort with significant background seroprevalence and incidence of breakthrough infection over a short time period. Prior infection and breakthrough infection induced higher anti-SARS-CoV-2 Ab responses at 3 months post vaccine against all widely circulating VOC. However, responses to Omicron BA.1 were low at three months regardless of hybrid immunity from prior exposure or breakthrough infection. Booster doses after AZD1222 should be considered in the African setting, even after natural infection, as future variants may be more pathogenic as well as immune evasive in the context of waning immunity.

Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) exhibits a high mutations rate and monitoring its spread and evolution is essential for global control of the pandemic. This study determined the SARS-CoV-2 variants circulating in Lagos, from July 2021 to January 2022, when the nation experienced its third and fourth waves.The study utilised archived SARS-CoV-2 positive samples and Midnight whole-genome sequencing workflow from Oxford Nanopore Technologies. Six hundred and sixty-six archived SARS-CoV-2 positive samples, 488 community testing and 178 travellers were analysed. Three hundred forty-one sequences samples were assigned lineages, but 327 sequences with doubly verified collection dates recreated the timeline. 86.5% of the samples came from persons between 16 and 60 years old. Two infections with the Omicron variant (BA.1) among community testers were detected in August 2021 and from seven outbound travellers in September 2021. An inbound traveller also had the Omicron variant (BA.1) in September 2021. Thirteen lineages of the Delta variant and four lineages of the Omicron variant were detected.We show that the Omicron variant was in Nigeria before November 2021 and could have caused the short reprieve between the third and fourth waves. Several lineages detected suggest several introductions, highlighting the need for surveillance.

Since 1985, there has been resurgence of yellow fever in Africa with outbreaks occurring in more than 33 countries. From that time, thousands of cases have occurred in Nigeria which is the most populous country in Africa. Semi-urban and urban centres across the country are densely populated, with numerous sparsely populated rural settings in every State, some of which contain heavy forests. A wide-range of vegetation zones exists which lead to smooth transition of several tropical climates. As a result, there is preponderance of Aedes species in many parts of the country especially during the rainy season when relative humidity is high. Vector control is not applicable to jungle yellow fever, but infection in human population can be prevented by vaccination. Yellow fever deaths were recently reported in Nigeria, causing panic and public outcry. This review highlights the epidemiological trajectory of yellow fever, the past, and the present and future efforts in the country with a view to providing in-depth knowledge of yellow fever activities in order to enhance public health.

Objective 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. Methods 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). Results 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). Conclusions 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.

Background: COVID-19 mortality rate has not been formally assessed in Nigeria. We therefore aimed to address this gap and identify associated mortality risk factors during the first and second waves in Nigeria. Methods: We conducted a retrospective cohort study using the national surveillance database between February 27, 2020, and April 3, 2021. The outcome was deaths amongst persons with a laboratory diagnosis of COVID-19. Incidence rates of COVID-19 death per 100,000 person-days were estimated. Adjusted negative binomial regression was used to identify factors associated with COVID-19 death, and presented as adjusted Incidence Rate Ratios (aIRR) with 95% confidence intervals (CI). Results: The first wave included 65,790 COVID-19 patients, of whom 994 (1∙51%) died; the second wave included 91,089 patients, of whom 513 (0∙56%) died. The incidence rate of deaths related to COVID-19 was higher in the first wave [54∙25 (95% CI: 50∙98-57∙73)] than in the second wave [19∙19 (17∙60-20∙93)]. Factors independently associated with increased risk of death in both waves were: age ≥45 years, male gender [first wave aIRR 1∙65 (1∙35-2∙02) and second wave 1∙52 (1∙11-2∙06)], being symptomatic [aIRR 3∙17 (2∙59-3∙89) and 3∙04 (2∙20-4∙21)], and being hospitalised [aIRR 4∙19 (3∙26-5∙39) and 7∙84 (4∙90-12∙54)]. Interpretation: The incidence rate of COVID-19 death in Nigeria was higher in the first wave, suggesting improved public health response and care during the second wave. Regional mortality differences suggest that policy makers focus on regional equity in access to testing and quality of care to mitigate the impact of another COVID-19 wave in Nigeria. Funding: None to declare. Declaration of Interest: None to declare. Ethical Approval: Ethical approval for the study was given by the Nigeria National Health Research Ethics Committee (NHREC/01/01/2007-22/06/2020).

The observed epidemiology of SARS-CoV-2 in sub-Saharan Africa has varied greatly from that in Europe and the United States, with much lower reported incidence. Population-based studies are needed to estimate true cumulative incidence of SARS-CoV-2 to inform public health interventions. This study estimated SARS-CoV-2 seroprevalence in four selected states in Nigeria in October 2020. We implemented a two-stage cluster sample household survey in four Nigerian states (Enugu, Gombe, Lagos, and Nasarawa) to estimate age-stratified prevalence of SARS-CoV-2 antibodies. All individuals in sampled households were eligible for interview, blood draw, and nasal/oropharyngeal swab collection. We additionally tested participants for current/recent malaria infection. Seroprevalence estimates were calculated accounting for the complex survey design. Across all four states, 10,629 (96·5%) of 11,015 interviewed individuals provided blood samples. The seroprevalence of SARS-CoV-2 antibodies was 25·2% (95% CI 21·8–28·6) in Enugu State, 9·3% (95% CI 7·0–11·5) in Gombe State, 23·3% (95% CI 20·5–26·4) in Lagos State, and 18·0% (95% CI 14·4–21·6) in Nasarawa State. Prevalence of current/recent malaria infection ranged from 2·8% in Lagos to 45·8% in Gombe and was not significantly related to SARS-CoV-2 seroprevalence. The prevalence of active SARS-CoV-2 infection in the four states during the survey period was 0·2% (95% CI 0·1–0·4). Approximately eight months after the first reported COVID-19 case in Nigeria, seroprevalence indicated infection levels 194 times higher than the 24,198 officially reported COVID-19 cases across the four states; however, most of the population remained susceptible to COVID-19 in October 2020.

The global community is facing a health crisis caused by coronavirus disease 2019 (COVID-19). The coronavirus pandemic is severely disrupting the global economy. Countries are battling to slow the spread of the virus by testing, employing contact tracing, restricting travel, quarantining citizens, and encouraging use of face mask, hand hygiene and social distancing measures. The lockdown imposed in many countries including Nigeria has resulted in increased cost and shortages of reagents and supplies worldwide. Due to the highly contagious nature of the disease, rapid rate of spread, and lack of an effective therapy, it became necessary for nations of the world to mount an efficient response mechanism to curb the spread of the pandemic. The Nigerian Institute of Medical Research (NIMR) has responded actively to the current pandemic with some innovations with respect to sample collection systems, molecular diagnostics, kit development and validation. Due to the highly infectious nature of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the causative agent of COVID-19, the institute also invested in the production of infection control tools. The extent of response by the institute would not have been possible but for collaboration and partnership with well-meaning organizations and stakeholders. National, State and public cooperation are very essential for effective response to any pandemic. The response of NIMR to the pandemic is herein discussed. Lessons learned and recommendations made are also shared to help institutions interested in combating this and future pandemics of similar nature.

To evaluate the effect of a combination of nevirapine + stavudine + lamivudine on Haematological and Biochemical values of HIV-1 positive patients in Lagos. Fifty patients who met the enrollment criteria for accelerated clinical trial were studied. Ten millimeters of blood was taken from each patient at first visit for basic haematological and biochemical values. Viral load and CD4 cell counts were also analyzed. All the values were repeated at 12 weeks, and 24 weeks, after patients were placed on drug treatment regimen. All the data were analyzed using Epi-info version 6.4D. The mean erythrocyte sedimentation rate (ESR) results were 53.3 ± 41.8 mm/1 hr, 48.2 ± 40.6 mm/1 hr and 28.6 ± 20.7 mm/1 hr. Haemoglobin (Hb) 123 ± 15 g/L, 124 ± 21 g/L and 132 ± 14 g/L. Packed cell volume 36.8 ± 4.5%, 37.6 ± 4.8%, and 40.3 ± 3.3%. Total white blood cell (WBC) 4.2 ± 1.0, 5.0 ± 1.5 and 4.6 ± 1.0 (baseline, 12 weeks and 24 weeks respectively). Creatinine, 1.2 ± 0.68 g/L, 1.2 ± 0.7 g/L and 1.04 ± 0.3 g/L at (baseline, 12 weeks and 24 weeks respectively). Serum amylase 37.9 ± 15.1 IU/L, 38 ± 23.9 IU/L and 24.3 ± 11.6 IU/L. Triglyceride 95.2 ± 48.3 IU/L, 92.38 ± 54.3 IU/L, and 78.0 ± 35.6 IU/L. Serum bilirubin 0.18 ± 0.09 μmol/L, 0.29 ± 0.28 μmol/L and 0.33 ± 0.24 μmol/L. Alanine transaminase (ALT) 9.9 ± 3.3 IU/L, 15.1 ± 9.0 IU/L and 14.1 ± 9.3 IU/L. Serum aspartate transaminase (AST) 8.2 ± 6.2 IU/L, 9.4 ± 5.2 IU/L and 9.1 ± 6.0 IU/L. On comparison of the results between baseline and 12th week, all parameter were similar except PCV, Hb, serum bilirubin, serum ALT, and total WBC, which were significantly high at 12th week. (p≤ 0.05). On comparison of results between 12th week and 24th week all parameters were similar except Hb and PCV (which were significantly higher at 24th week) while ESR, was significantly lower at 24th week (p≤ 0.05). It was concluded that nevirapine + stavudine + lamivudine combination results in improved haematological values of HIV/AIDS patients. The effect of the drug combination on biochemical parameter in a short period of 24 weeks may not be much. Clinical response and haematological response alone may be used for patient monitoring in a resource poor setting where CD4 count and viral load analysis is impossible.

This study investigated the diversity of rotavirus strains recovered from young children in Lagos, Nigeria, during December 1996-January 1997. In total, 287 children, aged 1-60 month(s), presenting with diarrhoea to the Gbaja Health Centre of Massey Street Children Hospital and the Lagos University Teaching Hospital, were included in the study. Rotavirus-positive specimens were characterized by monoclonal antibody enzyme-linked immunosorbent assay (ELISA) for VP6 subgroup and VP7 serotype and by polymerase chain reaction (PCR) for VP4 genotype and VP7 strains (that were non-reactive to ELISA). Of 84 samples tested for VP6 subgroup epitope, subgroup II was predominant (51%) with only a few subgroup I strains (4%), while many could not be typed at all (45%). For the VP7 serotypes, G1 was the most prevalent strain (45%), followed by G3 strains (5%). Neither G2 nor G4 strains were found, although mixed G1/G2 has been reported for the first time in Nigeria. Of strains that were non-reactive to ELISA, 29 (34%) could not be typed by PCR for G type. A subset of 23 samples was selected on the basis of RNA electropherotype, VP7 serotype, and included nine strains of VP7 that were non-reactive to ELISA. VP4 genotype of this subset was determined by PCR, and the most prevalent genotype was P[6] (30%), followed by P[8] (26%). Only one P[4] strain was identified. This study has shown the diversity of rotavirus strains circulating in West Africa.