The ongoing SARS-CoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing a severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months, between 14th February to 24th April 2020, using whole genome sequences. We performed recombination analysis against closely related CoV strains, Bayesian time scaled phylogeny, and investigation of spike protein amino acid mutations. Recombination signals were observed between the Afr-SARS-CoV-2 sequences and reference sequences within the RdRPs and S genes. The evolutionary rate of the Afr-SARS-CoV-2 was 4.133 × 10-4 Highest Posterior Density (HPD 4.132 × 10-4 to 4.134 × 10-4) substitutions/site/year. The time to most recent common ancestor (TMRCA) of the African strains was December 7th 2019, (95% HPD November 12th 2019-December 29th 2019). The Afr-SARCoV-2 sequences diversified into two lineages A and B, with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility (MCC) tree and PANGOLIN software. There was a high prevalence of the D614G spike protein amino acid mutation 59/69 (82.61%) among the African strains. This study has revealed a rapidly diversifying viral population with the G614G spike protein variant dominatinge advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARS-CoV-2 in Africa.

This study investigated measles infection in vaccinated and unvaccinated children presenting with fever and maculopapular rash during measles outbreaks in the southern and western states of Nigeria. Measles, an acute viral illness caused by a virus in the family Paramyxoviridae, is a vaccine-preventable disease. Measles outbreak is common in Nigeria, despite the national immunization program. Children presenting with symptoms of measles infection in general hospitals and health centers in the states of southern and western Nigeria were recruited for this study. Vaccination history, clinical details, and 5 mL of blood were obtained from the children. Their sera samples were screened for specific immunoglobulin M antibodies to measles virus. Of 234 children tested (124 [53.2%] female), 133 (56.8%) had previously been vaccinated against measles virus, while 93 (39.7%) had not been vaccinated. Vaccination information for eight children could not be retrieved. One hundred and forty-three (62.4%) had measles IgM antibodies. Of these, 79 (55.3%) had been vaccinated for measles, while 65 (44.7%) had not. Despite the ongoing vaccination program in Nigeria, a high number of children are still being infected with measles, despite their vaccination status. Therefore, there is need to identify the reason for the low level of vaccine protection.

INTRODUCTION: Hepatitis B virus (HBV) infection is a major health challenge in sub-Saharan African countries. Chronic HBV infection is a risk factor for severe disease progression. Perinatal and sexual transmissions of Hepatitis B virus are the main routes of infection in HBV endemic countries like Nigeria. However, there is paucity of data as regards the major contributory route of transmission to chronic HBV infection in this region. Also, in Nigeria, not everyone at high risk of the infection has been identified. Therefore our study investigated the prevalence of HBV infection among sexually active individuals in Nigeria. METHODS: blood samples collected from 463 participants (360 sexually active individuals and 103 teenagers) recruited from health institutions across the country were tested for the presence of HBsAg, and HBV nucleic acid related antigen (HBVNRAg) by ELISA. Positive samples were further tested for the presence of HBeAg and antiHBe by ELISA. Data were analyzed using Chi-square and binary logistic regression at p = 0.05. RESULTS: HBsAg and HBVNRAg were detected in 10.4% and 7.6% of the participants respectively. STI clinic attendees had the highest prevalence for HBsAg (17%; p = 0.002). Teenagers had the lowest HBsAg (1.9; p = 0.002) and HBVNRAg (2.9%; p = 0.0001) prevalence rates. Male gender (p = 0.01) and reproductive age group (p = 0.009) were the major predictors of chronic HBV infection. CONCLUSION: sexual transmission was identified as the major contributor to chronic HBV infection. Sexually active individuals especially those with STIs are high risk groups for chronic HBV infection. Interventions targeted at this group is therefore recommended.

Group A rotavirus (RVA) genotype G12 has spread globally and has become one of the most prevalent genotypes of rotavirus in Africa. To understand the drivers for its genetic diversity and rapid spread we investigated the Bayesian phylogeography, viral evolution and population demography of Rotavirus G12 in Africa. We downloaded and aligned VP7 gene sequences of Rotavirus genotype G12, from thirteen African countries (n = 96). Phylogenetic analysis, Evolutionary analysis and Bayesian Phylogeography was carried out, using MEGA Vs 6, BEAST, and SPREAD3. Phylogenetic analysis revealed that all the African sequences fell into lineage III diversifying into two major clades. The evolutionary rate of the African rotavirus G12 sequences was 1.678×10-3, (95% HPD, 1.201×10-3 - 2.198×10-3) substitutions/site/year, with TMRC of 16.8 years. The Maximum clade credibility (MCC) tree clustered into three lineages (II, III, IV), African strains fell within lineage III, and diversified into three clusters. Phylogeography suggested that South Africa seemed to be the epicentre of dispersal of the genotype. The demographic history of the G12 viruses revealed a steady increase between the years1998-2007, followed by a sharp decrease in effective population size between the years 2008-2011. We have shown the potential for genetic diversification of Rotavirus genotype G12 in Africa. We recommend the adoption of Molecular surveillance across Africa to further control spread and diversification of Rotavirus.

As a result of the ever increasing problem of multiresistant bacteria, we instituted a surveillance program with the aim of identifying the basic molecular properties of ESBL in our environment. About 197 isolates of Escherichia coli and Klebsiella pneumoniae were selected and tested for ESBL production and antimicrobial susceptibility. Plasmid profiles were determined and curing ability was tested. ESBL prevalence was 26.4% for all isolates tested, with E. coli having a greater proportion. There was absolute resistance to ampicilin, tetracycline, and co-trimaxole among tested isolates. There was above average susceptibility to the 2nd and 3rd generation cephalosporins. Plasmid profiles of tested isolates ranged from 9kbp to 26kbp with average of kbp for E. coli and kbp K. pneumoniae, 9.6% of ESBL positive E. coli plasmids were cured, while 3.9% of K. pneumoniae plasmids were cured after treatment. The present study shows an upsurge in ESBL acquisition by gram negative bacteria and evidence of cocirculation of varying subtypes of ESBL with both plasmid transmissible and chromosome encoded subtypes. This calls for universal surveillance and more effort towards molecular epidemiology of this public health treatment.

Background: West Nile virus (WNV) infection, is an arbovirus infection with high morbidity and mortality, the vector responsible for both human and animal transmission is Culex pipens complex. Objective: To determine the species distribution and seasonal abundance of Culex pipens and Culex quinquefasciatus mosquitoes in Abeokuta, Nigeria. Methods: Mosquitoes belonging to the Culex pipens complex were captured in three different locations located within Abeokuta Metropolis between March 2012 and January 2013. Individual species were identified using morphometric methods. Amplification of the Ace2 gene by PCR confirmed morphormetric identification of the mosquitoes. Results: A total of 751 mosquitoes were captured. Culex quinquefaciatus recorded the highest distribution of vectors with 56.6% and Culex pipens 43.4% (P > 0.05). Idi aba community recorded the highest distribution of mosquito vectors with 42.9% (n=322) and Culex quinqueaciatus was more abundantly distributed with 183 mosquitoes. Aro community recorded 32% (n=240) of captured mosquitoes with Culex quinquefaciatus having a higher level of abundance and lastly Kemta with a distribution of 25.1% (n=189). Conclusion: Results from this study show that potential vectors of WNV abound within Abeokuta, putting residents at high risk of West Nile infection. We advocate for introduction of routine testing of WNV in Abeokuta and Nigeria. Keywords: West Nile Virus, Culex pipens complex, PCR, Abeokuta