Group A rotaviruses circulating prior to a national immunization programme in Nigeria: Clinical manifestations, high G12P[8] frequency, intra-genotypic divergence of VP4 and VP7.

Nigeria having approximately 50 000 Rotavirus A (RVA) deaths annually is yet to introduce RVA vaccine into routine national immunization; therefore surveillance of RVA strains circulating before vaccine introduction is essential in evaluating impact of the intervention. Stool samples and sociodemographic data of diarrhoeic children, <5 years were collected between August 2012 and December 2013. While a high prevalence of RVA infection (47.6%; 49/103) was observed by quantitative reverse transcription real time PCR, only 25% (26/103) had high RVA genome concentrations and were antigen positive. G and P types were obtained for 31 and 37 samples respectively. G12P[8] strains were predominant (30.6%; 16/31); Other genotypes found included G9, G3, G2 and P[4], P[6], P[8]. A G12 + G2/P[8] + P[6] mixed infection was detected. The P[8] genotype showed divergence with strains distributed in lineage III and IV. Compared to the vaccines, changes in antigenic sites of VP8* and VP7 were found. The finding of the G2P[6] genotype combination and emergence of G12 strains support observations in most of the recent RVA studies from Africa. P[6] is common in many African countries, in contrast to countries in Europe and the Americas. In conclusion, this study shows the circulation of other RVA genotypes compared to the common RVA genotypes in Nigeria. PCR results should be interpreted with caution to avoid significant bias from samples with low RVA genome concentrations. These findings provide important information on the detection and molecular epidemiology of RVA prior to vaccination and contribute as a baseline for future evaluations after possible vaccine introduction.

Chikungunya Virus Seroprevalence and Associated Factors among Hospital Attendees in Two States of Southwest Nigeria: A Preliminary Assessment.

Chikungunya virus (CHIKV) is a re-emerging pathogen causing long-term polyarthritis and encephalitis. In conducting a preliminary investigation, we hypothesized that there is no serologic evidence of CHIKV infection among attendees of selected hospitals in Lagos and Osun States, Nigeria. Sera from 304 consecutively selected participants were screened for CHIKV IgG and IgM using ELISA. Findings were analyzed vis-à-vis participants' demographic and clinical data. Over 90.0% of the participants had never heard of CHIKV despite the fact that a large proportion of them (88.8%) had secondary/tertiary education. Overall, 41.8% were positive for, at least, one antibody type (IgG or IgM), while about 16.0% of the participants had dual seropositivity (CHIKV IgG and IgM) with gender as associated factor (odds ratio [OR]: 2.8, p = 0.03). Prevalence rates were 31.8% and 38.4% for CHIKV IgG and IgM, respectively. Only hospital location (Osogbo) was associated with CHIKV IgG (OR: 2.2, p = 0.009), while gender alone was associated with CHIKV IgM (OR: 3.0, p = 0.001). Participants seropositive for CHIKV antibodies were mostly adults (18-59 yrs) belonging to the active work-force; five (22.7%) and three (20.0%) of the pregnant participants had CHIKV IgG and IgM, respectively. Detection of CHIKV IgM in some participants might make them potentially infectious to the newborn and mosquito vectors. Importantly, participants positive for either IgG or IgM had fever (72.8%, 67.2%) and general body pains (61.7%, 57.6%), respectively. This ELISA-based study revealed serologic evidence of CHIKV infection among hospital attendees in Lagos and Osun states with the group-specific prevalence rates being considerably high. ABBREVIATIONS: Chikungunya virus (CHIKV); Chikungunya (CHIK); enzyme-linked immunosorbent assay (ELISA); immunoglobulin G or M (IgG/IgM); odds ratio (OR); non-structural proteins (nsP); hemagglutination inhibiting (HI); complement fixing (CF); neutralization test (NT); immunofluorescence assay (IFA); plaque reduction neutralization test (PRNT); confidence interval (CI); analysis of variance (ANOVA); body temperature (BT); Building Nigeria's Response to Climate Change (BNRCC).

Whole genome sequencing and phylogenetic analysis of SARS-CoV-2 strains isolated during the COVID-19 pandemic in Nigeria.

Objectives: The emergence and spread of SARS-CoV-2 have stimulated ongoing research into the virus transmission dynamics, circulating variants, and potential mutations. This study was conducted to understand the genomic dynamics of the epidemic in Nigeria. Design: Whole genome sequencing was conducted on SARS-CoV-2 samples collected during the first and second outbreaks using the Oxford Nanopore MinION sequencing platform. Phylogenetic analysis was conducted, and genomes were grouped into different pangolin lineages. Results: The study revealed four circulating SARS-CoV-2 variants. The Alpha (B.1.1.7) variant was the most prevalent (32.7%), followed by Beta (B.1 B.1.1, L.3, and B.1.1.318) (30.8%), Eta (B.1.525) (28.9%), and Delta (B.1.617, AY.1, AY.109, and AY.36) (7.7%). Phylogenetic analysis revealed three clusters with four Nextstrain clades (20I, 20B, 21D, and 21J). The Alpha lineages (B.1.1.7) clustered with references from Italy. The Beta lineages (Clade 20B) (B.11, B.11318, and L3) and sub-lineage B.11 were distinct. Sub-lineage B.11318 is clustered with references from the USA, whereas sub-lineage L3 is clustered with references from Russia, the Philippines, Australia, and Japan. The 21D and 21J, belonging to two Pango lineages, Eta (B.1525) and Delta (B.1.617 and AY.109), showed high genetic similarity. Conclusion: The phylogenetic relatedness of the lineages suggests multiple virus introduction, which could be a source of more virulent, locally adapted variants.

Butchering activity is the main risk factor for hepatitis E virus (Paslahepevirus balayani) infection in southwestern Nigeria: a prospective cohort study.

Introduction: Paslahepevirus balayani (Hepatitis E virus; HEV) is an emerging virus that poses as a public health threat. The virus is now reported to be the leading cause of acute viral hepatitis, with a unique impact on African settings. Our aim was to evaluate the prevalence and risk factors for HEV infection in three cohorts (animal handlers, villagers, and students). Methods: A prospective cross-sectional study was carried out on a total of 752 subjects from southwestern Nigeria. In all individuals, anti-HEV IgG and anti-HEV IgM antibodies were evaluated by using ELISA (confirming positive results via immunoblotting), and serum viral RNA was evaluated by using two RT-PCR assays. Results: The overall seroprevalence of HEV IgG and HEV IgM was 14.9% (95% CI: 12.5-17.6%) and 1.3% (95% CI: 0.7-2.5%), respectively. We observed the highest seroprevalence among animal contact individuals, with butchers being the population with the highest HEV IgG seroprevalence (31.1%). Similarly, HEV IgM was higher in the animal contact group (2.2%) than in the non-animal contact cohort (0%). Discussions: Viral RNA was not detected in any of the samples. Butchering was significantly associated with higher HEV prevalence. Although all efforts to prevent HEV in Africa have focused on the chlorination of water, our study suggests that most new infections could currently be linked to animal manipulation. Therefore, education and guidelines must be provided in southwest Nigeria to ensure that animal handling and processing methods are safe.

Genotypes and phenotypes of Shiga toxin-producing Escherichia coli (STEC) in Abeokuta, Southwestern Nigeria.

PURPOSE: To characterize the prevalence of hemolytic Shiga toxin-producing Escherichia coli (STEC) with a multidrug-resistant pattern in different age groups in Abeokuta, Nigeria. METHODS: Nonrepetitive E. coli isolates were collected from 202 subjects with or without evidence of diarrhea. Each isolate was biochemically identified and antimicrobial susceptibility testing was performed using the disk diffusion method. A sorbitol fermentation test of all the E. coli isolates was done and the minimum inhibitory concentration of suspected STEC was measured by the standard broth microdilution method to determine antibiotic resistance. The genotypes of stx1, stx2, and hlyA were determined by polymerase chain reaction assay. RESULTS: The majority of subjects were aged ≥40 years (41.6%) and were female (61.9%). Of the 202 subjects, 86.1% had STEC isolates (P<0.05). A high rate of STEC isolates resistant to amoxicillin (90.6%), cefotaxime (77.7%), and cefuroxime (75.7%) was observed. Resistance to amoxicillin, gentamicin, and cefotaxime was demonstrated with a minimum inhibitory concentration >16 µg/mL in 13.9%, 11.4%, and 10.4% of the isolates, respectively. The prevalence of stx1, stx2, and hlyA was 13.9%, 6.9%, and 2.0%, respectively; 5.5% of stx1 were in the 0-10-year-old age group, 3.5% of stx2 were aged ≥40 and above, and 1.0% of the hlyA isolates were in the 0-10-year-old age group. CONCLUSION: The prevalence of virulent STEC is a public health concern. The use of polymerase chain reaction assay should aid quick detection of this virulent serotype and help curb the severe epidemic of human diseases associated with STEC infections.