Prediction of malaria positivity using patients' demographic and environmental features and clinical symptoms to complement parasitological confirmation before treatment.

BACKGROUND: Current malaria diagnosis methods that rely on microscopy and Histidine Rich Protein-2 (HRP2)-based rapid diagnostic tests (RDT) have drawbacks that necessitate the development of improved and complementary malaria diagnostic methods to overcome some or all these limitations. Consequently, the addition of automated detection and classification of malaria using laboratory methods can provide patients with more accurate and faster diagnosis. Therefore, this study used a machine-learning model to predict Plasmodium falciparum (Pf) antigen positivity (presence of malaria) based on sociodemographic behaviour, environment, and clinical features. METHOD: Data from 200 Nigerian patients were used to develop predictive models using nested cross-validation and sequential backward feature selection (SBFS), with 80% of the dataset randomly selected for training and optimisation and the remaining 20% for testing the models. Outcomes were classified as Pf-positive or Pf-negative, corresponding to the presence or absence of malaria, respectively. RESULTS: Among the three machine learning models examined, the penalised logistic regression model had the best area under the receiver operating characteristic curve for the training set (AUC = 84%; 95% confidence interval [CI]: 75-93%) and test set (AUC = 83%; 95% CI: 63-100%). Increased odds of malaria were associated with higher body weight (adjusted odds ratio (AOR) = 4.50, 95% CI: 2.27 to 8.01, p < 0.0001). Even though the association between the odds of having malaria and body temperature was not significant, patients with high body temperature had higher odds of testing positive for the Pf antigen than those who did not have high body temperature (AOR = 1.40, 95% CI: 0.99 to 1.91, p = 0.068). In addition, patients who had bushes in their surroundings (AOR = 2.60, 95% CI: 1.30 to 4.66, p = 0.006) or experienced fever (AOR = 2.10, 95% CI: 0.88 to 4.24, p = 0.099), headache (AOR = 2.07; 95% CI: 0.95 to 3.95, p = 0.068), muscle pain (AOR = 1.49; 95% CI: 0.66 to 3.39, p = 0.333), and vomiting (AOR = 2.32; 95% CI: 0.85 to 6.82, p = 0.097) were more likely to experience malaria. In contrast, decreased odds of malaria were associated with age (AOR = 0.62, 95% CI: 0.41 to 0.90, p = 0.012) and BMI (AOR = 0.47, 95% CI: 0.26 to 0.80, p = 0.006). CONCLUSION: Newly developed routinely collected baseline sociodemographic, environmental, and clinical features to predict Pf antigen positivity may be a valuable tool for clinical decision-making.

Serological Investigation of Japanese Encephalitis Virus Infection in Commercially Reared Pigs, Southwestern Nigeria.

Japanese encephalitis virus (JEV) is a zoonotic arbovirus that causes abortion, stillbirth, and congenital defects in pigs, and epidemic encephalitis in humans. Currently, there is scarcity of information on JEV infection in pigs in Nigeria. Since the Culex tritaeniorhynchus vector of JEV is present in Nigeria and considering recent anecdotal reports of abortions and birth of weak piglets in some pig farms in southwestern Nigeria, there is a need for studies on the presence of the virus and its true burden among pig populations in the country. Serum samples (n=368) obtained from farm-reared pigs in four States of southwestern Nigeria were screened for JEV-specific IgG antibodies using a commercial ELISA kit. An overall JEV seropositivity of 35.1% (95% CI: 30.18 - 39.93%) was obtained, with detectable antibodies in pigs of all age groups, breeds, sex, and locations. Our results suggest natural exposure of these unvaccinated intensively reared pigs to JEV circulating silently in the swine population with significant association of the seropositivity with location (state/community in which the pig farms exist) and breed of the pigs studied. This first report of detection of anti-JEV antibodies in pigs in Nigeria indicates that JEV circulated among these pigs and underscores the need for active surveillance for JEV in humans, pigs, and mosquitoes to provide valuable epidemiological data for the design of effective control strategies against the virus, thus forestalling potential future outbreaks of the infection.

16S rRNA metagenomics data on the bacterial communities in integrated poultry-fish farm ponds.

In an integrated poultry-fish (IPF) farming system, fish and bird are reared simultaneously. It is a common practice in Sub-Saharan Africa countries like Nigeria, Cameroon, Madagascar, and Benin, offering economic benefits to farmers and minimizing farm running costs. It seems like another way for farmers to manage poultry waste as it is a common practice in IPF farm settings to feed reared fishes with wastes emanating from the poultry. This work provides dataset on the bacterial taxonomic profile and abundance in IPF farm pond water samples using the 16S rRNA sequencing approach. Using ZymoBIOMICS®-96 MagBead DNA Kit, total DNA was extracted from pond water samples collected from IPF farm located at Ila-Orangun, Osun State, Southwest Nigeria (Long: 8° 1' N; Lat: 4° 54' E) during two sampling visits. The V3-V4 region of the rRNA gene was amplified and sequenced on the Miseq Illumina sequencing platform. Raw reads obtained after demultiplexing were analyzed using DADA2 pipeline to obtain distinctive or unique amplicon sequence variants which were grouped into Operational Taxonomic Units (OTUs) based on similarities. Taxonomy assignment was performed using UCLUST and Bayesian classifier from QIIME v.1.9.1 with the Zymo Research Database as reference. The phyla Proteobacteria (26.7%), Actinobacteria (26.0%), Firmicutes (13.1%), and Cyanobacteria (10.1%) dominated the 35 phyla obtained from the OTUs. Interestingly, the abundance of bacterial pathogens commonly associated with human infections was low. The sequence and sample data have been deposited in NCBI database under Sequence Read Archive (SRA) with Bioproject identification number PRJNA760919 (Accession number: SRX12020336 - SRX12020346). The dataset obtained can bridge the gap of limited information on the impact of IPF farming on pond bacterial diversity, a critical factor for considerations as regards food safety, fish, and public health.

Multidrug-resistant enteric bacteria in Nigeria and potential use of bacteriophages as biocontrol.

Enteric bacterial pathogens have been implicated in many cases of gastroenteritis in Nigeria, a West African country. This situation is worsened by some reports of the high prevalence of multidrug-resistant enteric bacteria. To better prepare for situations in which even antibiotics of last resort would fail to treat infections caused by these pathogens, attention should be paid to alternative antimicrobial strategies. Here, we summarize existing reports of multidrug-resistant enteric bacterial infections in Nigeria, and importantly present the use of bacteriophages (viruses of bacteria) as an attractive antimicrobial alternative to combat these pathogens. It is hoped that this review will encourage research into the use of lytic bacteriophages against multidrug-resistant enteric bacteria in Nigeria.

Multiple Sexual Partners as Major Predictor of Human Immunodeficiency Virus Seropositivity Among Pregnant Women, Osun State, Nigeria.

Concerning human immunodeficiency virus (HIV) epidemiology, pregnant women (PW) are particularly vulnerable and severely affected. Nigeria has over 40 years of HIV epidemiology and enlightenments; to suggest control hub, we sought to know extant variables predicting HIV positivity among PW in selected towns in Osun State. Our hypothesis: none of the study PW's variables predicts HIV seropositivity. With ethics approval from UNIOSUN Health Research Ethics Committee, 900 consecutively selected consenting PW attending antenatal care (ANC) facilities in four towns (capital city inclusive) provided relevant sociodemographic/behavioral data with questionnaire forms; each participant was aseptically bled and plasma screened with the Alere Determine® Rapid HIV-1/2 Kit. The presumptive reactive plasma samples (and some randomly selected nonreactive samples) were confirmed with Genscreen® ULTRA HIV-1/2 P24 antigen/antibody ELISA. Microsoft Excel and SPSS 16.0 were used for result analysis using t-test, CHI2 test, and binary logistic regression. The PW were 15-50 years of age (n = 900; mean: 26.6 years [95% CI: 26.1-26.9 years]); they were predominantly 15-29 years (71.1%), married (90.8%), with one lifetime sexual partner (86.4%). Seropositive PW by screening and confirmatory tests were, respectively, 14 (1.6% [95% CI: 0.9-2.6%]) and 15 (1.7% [95% CI: 0.9-2.7%]). The latter were predominantly 20-30 years (80.0%), married (93.3%), with ≤ secondary school education (86.7%), reportedly never screened for HIV (60.0%), with 86.7% aware HIV is sexually transmitted. Analysis showed only ≥ three lifetime sexual partners was independently associated with HIV seropositivity (p = 0.03; odds ratio (OR) = 17.0). Although educational status was not associated with seropositivity, PW having primary school education had about 6 times higher likelihood of seropositivity (p = 0.06; OR = 5.7 [95% CI: 0.94-35.1]). Also, primigravida had about twice higher likelihood of seropositivity (p = 0.44; OR = 1.5 [95% CI: 0.54-4.17]). HIV seropositivity was relatively low and majorly predicted by ≥ three lifetime sexual partners; suggesting this as prime focus of HIV counseling among PW attending ANC in Osun State, Nigeria.

Real-time RT-PCR for COVID-19 diagnosis: challenges and prospects.

COVID-19 impacts global public health, economy, education, tourism/hospitality and sports; rapid and accurate testing of clinical samples dictate effective response. So far, the real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) is the assay of choice for COVID-19 diagnosis considering its rapidity and accuracy in informing on active coronavirus (CoV) infection. Presently, several RT-qPCR protocols with differing sensitivity/specificity are used for performing this assay; some of them are known to have generated debatable test results to constitute challenges worthy of consideration. This review provides a critical assessment of various published works on RT-qPCR assays used for COVID-19 diagnosis with their different indicators of positivity i.e., cycle threshold (Ct) cut-off values. Knowledge of diagnostic tests for COVID-19 is still evolving and, as a prospect, underscores the need for local validation of positive-negative Ct cut-off values when establishing RT-qPCR assays for SARS-CoV-2 detection.

Epidemiology and ecology of West Nile virus in sub-Saharan Africa.

West Nile virus (WNV) is the aetiological agent of the mosquito-borne zoonotic disease West Nile fever. The virus, first isolated in Uganda in 1937, evolved into two distinct lineages in sub-Saharan Africa (SSA) that subsequently spread to most continents where the virus has evolved further as evident through phylogenetic analysis of extant genomes. Numerous published reports from the past 70 years from countries in SSA indicate that the virus is endemic across the region. However, due in part to the limited availability of diagnostic methods across large areas of the continent, the human burden of WNV is poorly understood. So too are the drivers for translocation of the virus from countries south of the Sahara Desert to North Africa and Europe. Migratory birds are implicated in this translocation although the transient viraemia, measured in days, and the time taken to migrate, measured in weeks, suggest a more complex mechanism is in play. This review considers the evidence for the presence of WNV across SSA and the role of migratory birds in the emergence of the virus in other continents.

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).

Analysis of Culex and Aedes mosquitoes in southwestern Nigeria revealed no West Nile virus activity.

INTRODUCTION: Amplification and transmission of West Nile virus (WNV) by mosquitoes are driven by presence and number of viraemic/susceptible avian hosts. METHODS: In order to predict risk of WNV infection to humans, we collected mosquitoes from horse stables in Lagos and Ibadan, southwestern Nigeria. The mosquitoes were sorted and tested in pools with real-time RT-PCR to detect WNV (or flavivirus) RNA using WNV-specific primers and probes, as well as, pan-flavivirus-specific primers in two-step real-time RT-PCR. Minimum infection rate (MIR) was used to estimate mosquito infection rate. RESULTS: Only two genera of mosquitoes were caught (Culex, 98.9% and Aedes, 1.0%) totalling 4,112 females. None of the 424 mosquito pools tested was positive for WNV RNA; consequently the MIR was zero. Sequencing and BLAST analysis of amplicons detected in pan-flavivirus primer-mediated RT-PCR gave a consensus sequence of 28S rRNA of Culex quinquefasciatus suggesting integration of flaviviral RNA into mosquito genome. CONCLUSION: While the latter finding requires further investigation, we conclude there was little or no risk of human infection with WNV in the study areas during sampling. There was predominance of Culex mosquito, a competent WNV vector, around horse stables in the study areas. However, mosquito surveillance needs to continue for prompt detection of WNV activity in mosquitoes.

Epidemiological Evaluation of Rubella Virus Infection among Pregnant Women in Ibadan, Nigeria.

Rubella is a vaccine-preventable, mild rash-inducing viral disease with complications that include a spectrum of birth defects in the developing fetus, especially if the infection is acquired in the early months of pregnancy. Consequently, the primary objective of global rubella control programs is prevention of congenital rubella infection and associated birth defects. Despite the availability of safe and effective vaccines, and the elimination of the rubella virus in many developed countries, substantial commitment to rubella control has not been demonstrated in developing countries. This study appraises immunity to rubella, and consequently makes appropriate recommendations aimed at facilitating effective control. A cross-sectional sero-surveillance study was carried out among defined 272 consenting ante-natal clinic attendees in south-western, Nigeria. Prevalence rates of 91.54% and 1.84% were recorded for the anti-rubella virus (anti-RV) IgG and IgM, respectively. Also, 90.7% and 92.3% of the women aged ≤30 years and >30 years, respectively, had detectable anti-RV IgG. No significant association (p = 0.94) was recorded between anti-RV IgG detection and age of the women. Previous exposure and susceptibility of significant fraction of the population to rubella infection were confirmed. Considerable political commitment and promotion of free rubella immunization specifically for women with childbearing potential were recommended.

High seroprevelance of West Nile virus antibodies observed in horses from southwestern Nigeria.

To investigate exposure of Nigerian horses to West Nile virus (WNV), we determined the seroprevalence rate of anti-WNV antibody in a cohort of 145 horses. Serum samples were collected from three locations in southwestern Nigeria between October, 2011, and July, 2012. The horses were asymptomatic and unvaccinated against WNV at the time of sampling. All sera were tested using a competition enzyme-linked immmunosorbent assay (ELISA) and by an immunoglobulin M (IgM)-specific ELISA. High rates of anti-WNV antibody prevalence were observed in all locations with a mean level of 90.3% (95% confidence interval 84.3-94.6%). None of the horses had detectable anti-WNV IgM. This is the first ELISA-based report of WNV seroprevalence in Nigerian horses and suggests that WNV is enzootic in the study areas, indicating a potential risk of infection in humans and animals.

HBV Infection Among HIV-Infected Cohort and HIV-Negative Hospital Attendees in South Western Nigeria.

BACKGROUND: Prevalence, association and probable mode of acquisition of HBV and HIV dual infections have not been fully explored. Thus, HBV intervention plan and services are sometimes exclusively targeted towards HIV-infected population. We investigated HBV infection among HIV-infected cohort in comparison with HIV-negative hospital attendees to ascertain dual infectivity pattern; thereby encouraging appropriate allotment of intervention services. MATERIALS AND METHODS: A total of 349 (M=141; F=208; Mean=33.98 years; Range= 0.33-80 years) plasma specimens from two virus diagnostic laboratories in south-western Nigeria were analysed. These include 182 HIV-positive and 167 HIV-negative specimens from ART and GDV laboratories respectively. The specimens were initially screened for detectable HIV antigen/antibody, and subsequently HBsAg by ELISA technique. RESULTS: Overall, HBsAg was detected in 20.92% (95% CI: 16.65-25.19%) of the patients. Also, 24.82% (95% CI: 17.69-31.95%) and 18.27% (95% CI: 13.02-23.52%) HBsAg positivity was recorded for males and females respectively. CHI square analysis showed no association (P=0.14) between gender and prevalence of HBsAg. Similarly, comparison of prevalence of HBsAg by age groups shows no significant difference (P=0.24). Overall, no significant difference (P=0.59) was observed in the prevalence of HBsAg among the HIV-infected cohort and HIV-negative hospital attendees. CONCLUSIONS: Results of the study confirm endemicity and comparable rates of HBV infection independent of HIV-status.

High prevalence of anti-hepatitis A virus immunoglobulin G antibody among healthcare facility attendees in Osogbo, Nigeria.

The objectives of this study were to determine the prevalence of anti-hepatitis A virus (HAV) immunoglobulin G (IgG) antibody and associated factors among residents of Osogbo, a town in Nigeria with inadequate environmental sanitation and a shortage of potable water. This is a health facility-based study. Ninety one consenting, asymptomatic attendees of public healthcare facilities in Osogbo, Osun State, Nigeria, were consecutively selected for this study. Plasma samples of the study participants were tested for the presence of anti-HAV IgG using a HAV Ab Competitive Enzyme Immunoassay test kit. Ninety (98.9%) of the participants were seropositive for anti-HAV IgG antibody; group-specific prevalence was also high, but association of participants' variables with the prevalence could not be obtained due to limited sample size and high group-specific prevalence. Since the hepatitis A vaccine is not currently used in Nigeria, the chance is high that the HAV IgG antibody-positive individuals were naturally infected; consequently Osogbo can be described as highly endemic for HAV infection.

Dual positivity of hepatitis B surface antigen and anti-hepatitis C virus antibody and associated factors among apparently healthy patients of Ekiti State, Nigeria.

There are few studies on health-facility based prevalence rates for dual hepatitis B virus-hepatitis C virus (HBV-HCV) infection on a state-wide scale in Nigeria. In this study we determined the state-wide prevalence rate of dual positivity of hepatitis B surface antigen and anti-HCV antibody among hospital patients of Ekiti State, Nigeria, and identified associated factors. Consenting apparently-healthy patients visiting health centers in all local government area (LGA) headquarters of Ekiti State were consecutively selected to a total of 2000 individuals. Patient demographic data pertinent to HBV and HCV transmission were obtained using a structured questionnaire. Subsequently, serum samples prepared from the aseptically collected blood was tested for the presence of both HBsAg and anti-HCV antibody using DiaSpot test strips. The results were analyzed using binary logistic regression. Dual positivity of 7.40% was recorded among the study participants, with 9.80% and 12.80%, respectively, testing positive for HBsAg and anti-HCV antibody. The study patients were, however, most likely to be anti-HCV antibody positive. Nine of the 10 factors studied were independently associated with dual positivity. Five of these, in descending order of odds ratio, were: illiteracy (15.76, p=0.001); having ≥4 sexual partners (9.46, p=0.001); age range of 35-44 y (8.46,p=0.001); farming (7.33, p=0.001); and "not at all" to use of condoms during sexual intercourse (4.39, p=0.001). The dual positivity rate was relatively high, with unprotected sexual intercourse as the most probable mode of acquisition of HBV and HCV by the seropositive study participants.

CD4(+) T Cell Response to Lamivudine, Stavudine and Nevirapine in Human Immunodeficiency Virus Infected Antiretroviral-Naive Men in Nigeria.

Increase of (≥) 50 CD4(+) T cells/µl in post-commencement of highly active antiretroviral therapy (HAART) is acceptable as indicator of therapeutic success (TS). We therefore hypothesized that median change in CD4 count of the TS and therapeutic failure (TF) groups were comparable after 3 months; and that no associations existed between HAART outcome and adherence to therapy. One hundred Human immunodeficiency virus (HIV) infected antiretroviral (ARV) naive men on lamivudine + stavudine + nevirapine at Federal Medical Centre (FMC), Lokoja, Kogi State, Nigeria were studied. Data of the men were obtained with interviewer-administered questionnaire forms. Their ethylene diamine tetra acetic acid (EDTA)-treated whole blood samples were analysed with Partec CyFlow(®) Counter for pre-HAART and follow-up CD4 counts. Adherence to the ARV regimen was recorded for each patient as self-reported. We used Mann-Whitney U test, Kruskal-Wallis, Wilcoxon's matched pair and CHI(2) statistical tests for analyses. Overall adherence rate was 95.0%. Though the median follow-up CD4 count was higher (P = 0.001) than the pre-HAART value; only 85% of the men attained TS (increase of ≥50 cells/µl) at follow-up. Median change in CD4 count (+104.0 cells/µl; n = 85) of the TS was higher (P = 0.001) than that (-8.0 cells/µl; n = 15) of TF group; the two groups were however, comparable in age (P = 0.17) and body weight (P = 0.96). Only adherence and pre-HAART CD4 counts were associated (P = 0.001) with HAART outcome; while only age apparently influenced (P = 0.01) adherence rate. Eighty-five percent of the men benefited from the HAART. The success was apparently due to adherence and less than or (≤) 200 pre-HAART CD4 counts; while age ≥40 years appearently reduced adherence level.

Isolation of recombinant type 2 vaccine-derived poliovirus (VDPV) from a Nigerian child.

A type 2 vaccine-derived poliovirus (VDPV), differing from Sabin 2 at 2.5% (22/903) of VP1 nucleotide (nt) positions, was isolated from an incompletely immunized 21-month-old Nigerian child who developed acute flaccid paralysis in 2002. Sequences upstream of nt position 620 (within the 5'-untranslated region [5'-UTR]) and downstream of nt position 5840 (in the 3C(pro) region) were derived from species C enteroviruses unrelated to the oral poliovirus vaccine (OPV) strains. The two substitutions associated with the attenuated phenotype had either recombined out (A(481)-->G in the 5'-UTR) or reverted (Ile(143)-->Thr in VP1). The VDPV isolate had lost the temperature sensitive phenotype of Sabin 2 and it was antigenically distinct from the parental OPV strain, having amino acid substitutions in or near neutralizing antigenic sites 1 and 3. The date of the initiating OPV dose, calculated from the number of synonymous substitutions in the capsid region, was estimated to be approximately 16 to 18 months before onset of paralysis, a finding inconsistent with the most recent mass OPV campaign (conducted 12 days before onset of paralysis) as being the source of infection. Although no related type 2 VDPVs were detected in Nigeria or elsewhere, the VDPV was found in an area where conditions favor VDPV emergence and spread.