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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.

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.