Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria.

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 SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) 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 in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Spatum smear positive tuberculosis among tuberculosis patients in a sub-urban hospital in Northeastern Nigeria

Background: The global tuberculosis control strategy recommended by the World Health Organization. (WHO) directly observed therapy short Course (DOTS), is based on identification of sputum smear-positive pulmonary tuberculosis cases. The rate of sputum smear- positive tuberculosis has never been reported from this part of the country. Aim: To determine the prevalence of sputum smear positive tuberculosis. Materials and Methods: The study group comprised patients aged 14 years and above admitted either into the Infectious diseases or medical wards of the Federal Medical Centre, Nguru northeastern Nigeria from 1st January 2002 to 31st December 2002. Diagnosis of TB was based either on the detection of acid- and alcohol-fast bacilli on the sputum of suspected cases or the non-resolution of radiographic features following a course of broad spectrum antibiotic. All cases had sputum smear examination of three early morning specimens (5-10 ml each) by the Ziehl-Neelsen technique for the detection of tubercle bacilli. Results: Fifty five patients with TB comprising 37 (67.3%) males and 18 (32.7%) females qualified for the study out of which one (1.8%) had extra pulmonary TB. Their ages ranged between 14 and 75 years with a mean of 35.6 ± 12.4 years. Thirty five patients (63.6%) had positive sputum smears for Mycobacterium tuberculosis, out of which 26(74.3%) were males. Twenty (36.4%) had negative smears. Conclusion: There is a high rate of sputum smear positive tuberculosis among patients seen in this hospital and this may pose some risk to close contacts and care givers. Nigerian Journal of Health and Biomedical Sciences Vol. 7 (1) 2008 pp. 72-

The diversity of meningococcal carriage across the african meningitis belt and the impact of vaccination with a group a meningococcal conjugate vaccine

Background. Study of meningococcal carriage is essential to understanding the epidemiology of Neisseria meningitidis infection. Methods. Twenty cross-sectional carriage surveys were conducted in 7 countries in the African meningitis belt; 5 surveys were conducted after introduction of a new serogroup A meningococcal conjugate vaccine (MenAfriVac). Pharyngeal swab specimens were collected, and Neisseria species were identified by microbiological and molecular techniques. Results. A total of 1687 of 48 490 participants (3.4%; 95% confidence interval [CI], 3.2%-3.6%) carried meningococci. Carriage was more frequent in individuals aged 5-14 years, relative to those aged 15-29 years (adjusted odds ratio [OR], 1.41; 95% CI, 1.25-1.60); in males, relative to females (adjusted OR, 1.17; 95% CI, 1.10-1.24); in individuals in rural areas, relative to those in urban areas (adjusted OR, 1.44; 95% CI, 1.28-1.63); and in the dry season, relative to the rainy season (adjusted OR, 1.54; 95% CI, 1.37-1.75). Forty-eight percent of isolates had genes encoding disease-associated polysaccharide capsules; genogroup W predominated, and genogroup A was rare. Strain diversity was lower in countries in the center of the meningitis belt than in Senegal or Ethiopia. The prevalence of genogroup A fell from 0.7% to 0.02% in Chad following mass vaccination with MenAfriVac. Conclusions. The prevalence of meningococcal carriage in the African meningitis belt is lower than in industrialized countries and is very diverse and dynamic, even in the absence of vaccination