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

Evidences of endemic Schistosoma haematobium infection among School Children in Shonga Community, Edu Local Government Area, Kwara State, Nigeria

A study was carried to determine the presence, level of endemicity and the intensity of human Schistosoma haematobium infection in Shonga community of Edu Local Government Area in Kwara State, Nigeria. For permission and maximum cooperation, intensive advocacy and mobilization of the community leaders, school authorities and the pupils preceded the collection of urine specimens which were preserved in 10% alcohol. Microscopic examinations were carried out on the urine specimens. Conclusive diagnosis was based on the characteristic terminal spined egg of S. haematobium. Altogether, 1,479 pupils (60.0% boys and 40.0% girls), aged between 4-20 years, were examined in the over sixteen schools in and around the community, selected by convenience. Of all the pupils examined, 1,144 (77.4%) had the characteristic eggs of S. haematobium in their urine samples. Infection rate for boys was 516 (45.1%) while it was 296 (25.9%) for girls. Thus, boys were significantly more infected than girls (P<0.05). Children between 11-13 years of age had the highest prevalence of infection (47.2%) while those between 4-7 years of age had the least prevalence (30.0%). The overall mean egg-count for the 1,144 infected pupils was 1,598.0±49.32, while the mean egg-counts for boys and girls were 1,213.0±25.6 and 685.0±18.3 respectively. The difference in the intensity of infection between boys and girls was also significant (p<0.05). Of the 1,144 pupils who were infected with S. haematobium 195 (17.0%) had egg-count range of 1-1000, 758 (66.3%) had egg-count range of 1001-5000 while 191 (16.7%) had egg-count range of ≥5001. The prevalence of haematuria was also significantly higher among boys than girls (p<0.05). This study reveals that human Schistosoma haematobium infection is endemic in Shonga community. The awareness about the impact, transmission and prevention of this infection was relatively poor. Research on vaccine development to support the existing chemotherapy for the control and possible elimination of this dreaded but highly neglected parasitic infection should be the priority. Therefore, advocacy, health education chemotherapy and vaccine most be adopted concurrently as the best intervention strategy/approach to eradicate Schistosomiasis.Keywords: Schistosoma haematobium, prevalence, infection, endemicity, intensit

Epidemiology and clinicopathological manifestation of resurgent highly Pathogenic Avian Influenza (H5N1) virus in Nigeria, 2015

In January, 2015 the National Veterinary Research Institute, Vom, Nigeria received some chicken carcasses from the Kano state Ministry of Agriculture. The carcasses were from a backyard-commercial poultry farm and a live bird market (LBM) in Kauna and Sabon gari, Kano state, northwestern Nigeria respectively. The farm kept  different types of chickens of various ages and stages and was experiencing high mortality of 350 birds daily with eventual 100% mortality observed in the older birds (54weeks). In a concurrent incidence, reports were received of unusual high mortality of birds brought from the northern part of the country at two LBMs in  Onipanu and Mushin, Lagos state, southwestern Nigeria. A total of 8 chicken  carcasses from the Kano suspicion were subjected to postmortem examination and testing. One broiler-chicken (4weeks old), 4 layer-chicken (22 weeks old) and 3 indigenous bred-chickens (from LBM) showed severe pathological lesions  consistent with highly pathogenic avian influenza (HPAI). Moribund birds from the Lagos suspicion had cyanotic comb and wattles, torticollis and paralysis of the limbs. Parenchymatous organs, nasal and trachea swabs were collected from the dead and moribund birds respectively. The specimens were analyzed by RT-PCR and virus isolation in embryonating chicken eggs. All samples were found to be positive for HPAI (H5N1) subtype. This marks the re-introduction of HPAI (H5N1) subtype into Nigeria for a second time in the space of 9-years. So far, over 542 cases (January to December, 2015) have been confirmed positive for HPAI (H5N1) in 20 states of the country. Possible circumstances surrounding the resurgent and spread are discussed herein.Key words: Epidemiology, Resurgent HPAI H5N1, Pathology, Nigeria