VP7, VP4, and NSP4 genes of species a rotaviruses isolated from sewage in Nigeria, 2014/2015: partial sequence characterization and biophysical analysis of NSP4 (enterotoxin).

Species A rotavirus are an important cause of childhood gastroenteritis, and the main contributor to its pathogenicity is the enterotoxin (NSP4) protein. Some biophysical properties of partial NSP4 genes of RVAs isolated from sewage in Nigeria during 2014/2015 were investigated. Samples were typed by RT-PCR and Sanger sequencing of partial VP4, VP7 and NSP4 genes. Phylogeny identified lineages within genotypes, predicted glycosylation sites; hydrophobicity profiles and amino acid alignments were employed to determine some biophysical properties of the NSP4 protein. The VP7 sequences of our isolates were the most diversified, the majority of the isolates carried NSP4 genes of the E1 genotype. Genotype specific variations both in hydrophobicity and potential glycosylation were identified, mutations were highest within the H3 hydrophobic domain and VP4 binding domain. The study of RVA NSP4 genes from non-clinical samples revealed that there were structural consistencies with those of reference genes.

Genotypes of rhinovirus detected among children in two communities of South-West Nigeria.

Rhinoviruses (RVs) are the most common etiological agent implicated in respiratory infections among infants and children. There are currently no approved antivirals and vaccine for use against the virus; hence, the need for information on the genotypes of rhinovirus from developing countries of the world with high burden of the infection. This study determined the genotypes of rhinovirus circulating among children in selected cities in Nigeria. Nasopharyngeal and oropharyngeal samples were carefully collected from children showing signs of respiratory infection in two communities in South-west Nigeria. Polymerase Chain Reaction was used to amplify the hypervariable part of the 5'- non-coding region, the entire viral protein gene 4 and the 5' terminus of the VP2 gene of RV. Nucleotide BLAST and phylogenetic analyses were used to genotype the isolates. Of the samples analysed, 12.7% showed rhinovirus positivity. All the three genotypes of rhinovirus were detected with genotype C (71.4%), being the predominant. Multiple strains of rhinovirus were found circulating. We showed for the first time the genotypes and strains of rhinovirus circulating in Nigeria. Further studies are required to highlight transmission patterns and disease severity among rhinovirus species in Nigeria.

Profiles of mutations in hepatitis B virus surface and polymerase genes isolated from treatment-naïve Nigerians infected with genotype E.

Introduction. Hepatitis B virus (HBV) infection is the leading cause of hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). HBV genotype E (HBV/E) is the predominant genotype in West Africa and has been linked epidemiologically with chronic and occult HBV infections as well as development of HCC. Mutations in the surface and polymerase genes of HBV have been associated with occult infection, drug resistance, vaccine escape, as well as HCC.Hypothesis/Gap Statement. There is limited data on the occurrence and patterns of mutations associated with occult infection, drug resistance, vaccine escape and HCC for HBV/E.Aim. This study characterized amino acid (aa) substitutions in the major hydrophilic (MHR) and reverse transcriptase (RT) regions of the surface and polymerase genes respectively of HBV sequences from a group of Nigerians with genotype E infection. The CpG islands of the PreC/C and PreS/S regions of these sequences were also described.Methodology. HBV surface and polymerase genes were detected using PCR techniques. Occurrence of new and previously described mutations in these genes were analysed using phylogenetic techniques.Results. Overall 13 HBV isolates were each sequenced for polymerase and surface genes mutations. Thirteen and nine PreS/S and PreC/C HBV genes respectively were analysed for CpG islands. Mutations in the MHR and a-determinants region of the S protein were discovered in eleven and nine of the 13 tested isolates respectively. These mutations were concomitant with aa changes in the RT functional domains of the isolates. Mutations associated with vaccine escape, occult infection and poor HCC prognosis were identified in HBV/E isolated in this study. Furthermore, all the isolates had at least one putative nucleotide analogue resistance mutations. Drug resistance mutations had the highest association with CpG islands.Conclusion. The results of this study contribute to further understanding of HBV variability in Nigeria and the West African region. This will aid the planning of adequate HBV immunization and treatment programmes for the countries in the region.

Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats.

Bats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution of betacoronavirus (ßCoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell within Norbecovirus subgenera, with an evolutionary rate of 1.301 × 10-3, HPD (1.064 × 10-3-1.434 × 10-3) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus, Hibecovirus and Merbecovirus. The time to most common recent ancestor for Norbecovirus strains was 1973, and 2007, for the African Merbecovirus strains. There was evidence of inter species transmission of Norbecovirus among bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of ßCoV among African bats; we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population.

Dynamics of CD4 cell count among HIV-infected individuals in Lagos, Nigeria.

Human immunodeficiency virus (HIV) infection leads to progressive loss of CD4 T cells. Antiretroviral therapy has been able to inhibit this process, resulting in significant level of immune recovery and function. Our aim is to investigate the dynamics of CD4 recovery among HIV patients in Lagos, Nigeria. A total of 213 HIV-positive individuals were enrolled between October 2007 and May 2008, and followed up for 9 months based on CD4 count. CD4 analysis was done by flow cytometry at enrollment and after every 3 months. Data were grouped according to age range, antiretroviral treatment (ART), and time between infection and diagnosis. Kaplan-Meier survival analysis was used for data analysis. There was a significant difference in CD4 count between antiretroviral (ART) naïve and ART experienced subjects (P < 0.001). About 50% of the ART experienced population was identified to show poor CD4 reconstitution unable to achieve a CD4 of 500 cells/µl after 9 months of therapy. Time interval between infection and therapy was also identified to contribute to poor CD4 restoration. Further studies need to be done to classify immunological nonresponders among HIV patients in Nigeria. We also recommend introduction of programs that will facilitate early detection of HIV infection.

High-level Multi-Resistant and Virulent Escherichia coli in Abeokuta, Nigeria.

Multi-resistant Escherichia coli (E. coli) strains co-harboring virulence genes is a cause of high morbidity in Abeokuta, Nigeria. This study was designed to determine some virulent factors among enteropathogenic E. coli in Abeokuta, Nigeria. Approximately non-repetitive 102 isolates of E. coli were recovered from clinical samples from two health facilities in Abeokuta. Biotyping using API and antibiotic susceptibility was determined, and eae and flic genes were assayed by PCR. Antibiotic resistance relatedness was performed by DendroUPGMA. Results showed that 48.0% and 52.0 % were intestinal and extra-intestinal E. coli, ampicillin recorded 100% resistance, amoxycilli/clavulanic acid 64.7%, cotrimoxazole 57.8% and 56.8% resistance against cefotaxime, at MIC >16 ug/mL, 100%, 57.8%, and 50% have MIC50 to ampicillin, tetracycline, and ceftazidime, while 74.5% and 48.0% have MIC90 to ampicillin and ceftazidime. Significant rates of 4.9%, 7.8%, and 9.8% flic, eae, and flic/eae genes were found in intestinal isolates, while 2.9%, 2.0%, and 3.9% were found in extra-intestinal (P < 0.05). Two major clades of the resistant isolates reveal significant antibiotic relatedness among intestinal and extra-intestinal isolates, at 54% resistance similarities with very high multi-antibiotic resistance index of 1.0 (MARI). A high rate of undetected virulent E. coli pathotypes with high resistance could trigger unprecedented morbidity and mortality, mostly among children and the elderly.

Measles Virus Infection Among Vaccinated and Unvaccinated Children in Nigeria.

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.

Seroprevalence rates of hepatitis C virus (HCV) antibody and hepatitis B virus surface antigen (HBsAG) in blood donors in a Southwestern Nigerian city.

Hepatitis B and C have been identified as major causes of Transfusion transmitted infections, in Nigeria. Our objective was to determine the prevalence of Hepatitis B virus (HBV) and Hepatitis C virus (HCV) in prospective blood donors in Abeokuta, Nigeria. 305 blood donors were screened for the presence of Hepatitis B virus surface antigen (HBsAg) and HCV using a rapid immunochromatographic kit (DiaSpot®). Demographic information was also collected. Males constituted 96.4%, singles were the majority with 65%. Prevalence of HBsAg was 9.8%, HCV 1.3%, and dual positivity 0.3%. Prevalence of HBsAg and HCV among males was 10.2% and 1.4%, while females recorded 0.0% for HCV and HBsAg. Dual positivity was recorded in a male (0.33%). Analysis of the study variables revealed that only educational status was statistically associated with positivity of HBsAg [Formula: see text], HCV prevalence was highest in the illiterate group it was not statistically significant (P > 0.05). We report the prevalence rates of anti-HCV Ab and HBsAg in blood donors from Ogun State, Nigeria. Our results reveals higher rate of HBsAg and evidence of co-infection with both viruses, illiteracy was the only variable associated with HBV infection. We advocate for the inclusion of anti-HBc or HBeAg in donor screening in our environment.

A Multicenter Study of Beta-Lactamase Resistant Escherichia coli and Klebsiella pneumoniae Reveals High Level Chromosome Mediated Extended Spectrum ß Lactamase Resistance in Ogun State, Nigeria.

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 9 kbp to 26 kbp with average of 14.99 ± 2.3 kbp for E. coli and 20.98 ± 1.8 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.

Evaluation of IgG Antibodies Against Respiratory Syncytial Virus (RSV), and Associated Risk Factors for Severe Respiratory Tract Infections in Pre-School Children in North-Central, Nigeria.

BACKGROUND: Childhood mortality and morbidity due to RSV is increasing. Our current study was aimed at determining the sero-prevalence rate of RSV IgG antibodies and investigates certain known risk factors for RSV disease severity in infants and pre-school children presenting with various forms of respiratory tract infections in Ilorin, Nigeria. MATERIALS AND METHODS: About 280, children and 30, aged matched controls were enrolled into the study at the specialist hospital Ilorin. Blood testing for anti RSV IgG was done using a commercial ELISA kit by IVD Research Inc® Carlsbad. California U.S.A. Information regarding Nutritional status, socio-economic status and other demographic variables were collected. RESULTS: A prevalence rate of 85.7% was recorded among tested children and 23.3%, in controls, across age groups and gender. A statistically significant difference in age groups were recorded among patients with LRTI, (p <0.05), age <1 41%, age 1 <5, 27.6%. This was also the case for children with SRTI (Pneumonia and Bronchiolitis), with age < 1yr, 9%, and 1 <5yr, 19.8%. Analysed risk factors for disease severity showed thatnutritional status of children were statistically significant for disease severity, p-value, 0.039 (Chi square test). CONCLUSIONS: We report a high level of exposure to RSV in infancy and early childhood among children from a representative population in a major central Nigerian City, further studies into neutralising antibody levels and subtype distribution of RSV are advocated.

Evaluation of IgG antibodies against respiratory syncytial virus (RSV), and associated risk factors for severe respiratory tract infections in pre-school children in North-central, Nigeria

Background: Childhood mortality and morbidity due to RSV is increasing. Our current study was aimed at determining the sero-prevalence rate of RSV IgG antibodies and investigates certain known risk factors for RSV disease severity in infants and pre-school children presenting with various forms of respiratory tract infections in Ilorin, Nigeria. Materials and Methods: About 280, children and 30, aged matched controls were enrolled into the study at the specialist hospital Ilorin. Blood testing for anti RSV IgG was done using a commercial ELISA kit by IVD Research Inc® Carlsbad. California U.S.A. Information regarding Nutritional status, socio-economic status and other demographic variables were collected. Results: A prevalence rate of 85.7% was recorded among tested children and 23.3%, in controls, across age groups and gender. A statistically significant difference in age groups were recorded among patients with LRTI, (p <0.05), age <1 41%, age 1 <5, 27.6%. This was also the case for children with SRTI (Pneumonia and Bronchiolitis), with age < 1yr, 9%, and 1 <5yr, 19.8%. Analysed risk factors for disease severity showed thatnutritional status of children were statistically significant for disease severity, p-value, 0.039 (Chi square test). Conclusions: We report a high level of exposure to RSV in infancy and early childhood among children from a representative population in a major central Nigerian City, further studies into neutralising antibody levels and subtype distribution of RSV are advocated