A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.

Assessment of immunity against Yellow Fever virus infections in northeastern Nigeria using three serological assays.

Poor systematic surveillance for Yellow Fever virus (YFV) is primarily due to lack of affordable diagnostic facilities in resource-constrained countries. This study aimed at providing evidence-based information on immunity against Yellow Fever with a view to assessing the possibility of the recent epidemics persisting in Nigeria. Six hundred patients with febrile illness seeking malaria test in selected hospitals were tested for YFV antibody using three serological assays: ELISA IgM, microneutralization test (MNT) and plaque reduction neutralization test (PRNT). The three assays commonly detected YFV antibody (Ab) in 1.7% patients, MNT: IgM in 8.3%, IgM: PRNT in 7.1%, and MNT: PRNT in 3.2%. Immunity against YF was significantly higher in Bauchi and Borno than Adamawa and children aged 0-9 years compared to 20-29 years. YFV neutralizing antibody (nAb) strongly correlated with the vaccination status of the patients. More unvaccinated patients had nAb compared with the vaccinated. Immunity against YF among treated patients with antibiotic and/or antimalaria before sample collection inversely correlated with the untreated. YVnAb among unvaccinated indicates natural infections. Acute YFV infections were mistaken for malaria and natural infections are ongoing. Individuals aged more than or equal to 20 years should be targeted during mass vaccination campaigns. With low population immunity, repetitive YF epidemics in Nigeria is not yet over. The current policy on Yellow Fever vaccination in Nigeria still leaves a large unimmunized population at the risk of epidemics. Sufficient mass vaccination in combination with National Programme on Immunization remains key to averting YF epidemics.

Implications of SARS-CoV-2 genetic diversity and mutations on pathogenicity of the COVID-19 and biomedical interventions.

OBJECTIVE: Coronavirus disease 2019 (COVID-19) has caused an unprecedented global health emergency. The COVID-19 pandemic has claimed over 350,000 human lives within five months of its emergence, especially in the USA and the European continent. This study analysed the implications of the genetic diversity and mutations in SARS-CoV-2 on its virulence diversity and investigated how these factors could affect the successful development and application of antiviral chemotherapy and serodiagnostic test kits, and vaccination. METHODS: All the suitable and eligible full text articles published between 31st December 2019 and 31st May 2020 were filtered and extracted from "PubMed", "Scopus", "Web of Science", and "Hinari" and were critically reviewed. We used the Medical Subject Headings (MeSH) terms "COVID-19, "Mutation", "Genetic diversity", "SARS-CoV-2", "Virulence", "Pathogenicity", "Evolution" and "SARS-CoV-2 transmission" for this search. RESULTS: Our search showed that SARS-CoV-2 has persistently undergone significant mutations in various parts of its non-structural proteins (NSPs) especially NSP2 and NSP3, S protein, and RNA-dependent RNA polymerase (RdRp). In particular, the S protein was found to be the key determinant of evolution, transmission, and virulence of SARS-CoV-2, and could be a potential target for vaccine development. Additionally, RdRp could be a major target in the development of antivirals for the treatment of COVID-19. CONCLUSION: Given the critical importance of mutations in the pathogenicity of SARS-CoV-2 and in the development of sero-diagnostics, antivirals, and vaccines, this study recommends continuous molecular surveillance of SARS-CoV-2. This approach would potentially prompt identification of new mutants and their impact on ongoing biomedical interventions and COVID-19 control measures.

Prevalence of locally undetected acute infections of Flaviviruses in North-Eastern Nigeria.

The burden of Arboviral infections is largely underestimated in Africa, particularly in North-Eastern Nigeria. A total of 200 serum samples were collected from patients exhibiting febrile illness who visited the State Specialist Hospital in Maiduguri for medical attention between March and April 2018. Sera were tested for Flavivirus RNA by a pan-flaviviral primer set using hemi-nested RT PCR. Twenty-six samples were positive for flaviviral RNA and sequence analysis indicated a high number of West Nile virus infections and one case of Zika virus. In-house recombinant NS1-based IgM ELISA indicated 47 % of WNV and 22 % of ZIKV infections. These data were also compared to commercially available assays for West Nile and Zika viruses. Finally, NS1 IgG ELISA was conducted for Dengue, Zika, West Nile and Usutu viruses. For serum samples detected by at least one flavivirus, 945% tested positive by NS1 IgG antibodies, while only 5.5 % of the patients were negative for all. To conclude, there is a high prevalence rate of arbovirus infections in the region, including Zika and Usutu viruses that were not previously detected. Interestingly, the analysis was conducted using in-house tools to allow the implementation of a sustainable surveillance protocol locally.

Molecular characterization of group A rotavirus strains detected in children with diarrhea admitted to Nigerian hospitals in 2013.

Group A rotaviruses (RVA) are the leading cause of acute gastroenteritis (AGE) in children worldwide and cause up to 455,000 deaths annually, mostly in developing countries. During 2013, 66 RVAs from children with AGE admitted to four Nigerian hospitals were investigated. The G3P[6], G1P[8] and G2P[4] genotypes predominated. The VP7 and/or VP4 genes of 18 G3P[6]/[8]/[4], six G2P[4], three G12P[8]/[4], and two G1P[8] RVA strains were sequenced. The G3P[6] strains belonged to lineage G3-III and were different from G3 strains widespread in Asia. Phylogenetic analysis revealed substantial sequence conservation, suggesting continuing evolution and genomic reassortment but no zoonotic RVA transmission from animals.

Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent in enteric infections.

A new species of parvovirus, tentatively named human bocavirus 4 (HBoV4), was genetically characterized. Among 641 feces samples obtained from children and adults, the most commonly detected bocavirus species were, in descending order, HBoV2, HBoV3, HBoV4, and HBoV1, with an HBoV2 prevalence of 21% and 26% in Nigerian and Tunisian children, respectively. HBoV3 or HBoV4 species were found in 12 of 192 patients with non-polio acute flaccid paralysis in Tunisia and Nigeria and 0 of 96 healthy Tunisian contacts (P = .01). Evidence of extensive recombination at the NP1 and VP1 gene boundary between and within bocavirus species was found. The high degree of genetic diversity seen among the human bocaviruses found in feces specimens, relative to the highly homogeneous HBoV1, suggest that this worldwide-distributed respiratory pathogen may have recently evolved from an enteric bocavirus after acquiring an expanded tropism favoring the respiratory tract. Elucidating the possible role of the newly identified enteric bocaviruses in human diseases, including acute flaccid paralysis and diarrhea, will require further epidemiological studies.