Molecular detection of SARS-CoV-2 infection in three geo-political zones of Nigeria: a cross-sectional study

Introduction

sequel to the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its subsequent spread to all continents of the world, humans have continued to experience severe devastation to their health and economies. To control the spread of this virus, it is important to detect the infection in recently infected and asymptomatic individuals who are capable of infecting others. This study was designed to detect ongoing SARS-CoV-2 Infection among asymptomatic individuals in open markets across three geopolitical zones in Nigeria.

Methods

nasal and oropharyngeal swab samples were collected from 2,158 study participants between December 20^th, 2020 and March 20^th, 2021 from large open markets across three geo-political zones (Southwest, Northwest and Southeast) of Nigeria. Virus RNA was extracted from these swab samples and real time reverse transcription polymerase chain reaction (RT-PCR) was carried out for the detection of SARS-CoV-2 specific genes. Data were analysed using descriptive statistics.

Results

a total of 163 (7.6%) of the 2,158 participants enrolled for the study tested positive for SARS-CoV-2 by RT-PCR. The rate of infection was significantly higher in the North-western States of the country when compared to the western and Eastern regions (P=0.000). Similarly, the rate of infection was higher among buyers than sellers (P=0.000) and among males when compared with females, though the difference was not significant (p=0.31).

Conclusion

this study shows that there is a continuous spread of SARS-CoV-2, especially among active, asymptomatic individuals across many States in the country. There is therefore need to continuously educate citizens on the need to adhere to both the non-pharmaceutical and pharmaceutical preventive measures to protect themselves and ultimately curb the spread of the virus.

Human rotavirus VP4 and VP7 genetic diversity and detection of GII norovirus in Ibadan as Nigeria introduces rotavirus vaccine

Objective

This cross-sectional study investigated the circulating strains of rotavirus and screened for noravirus in Ibadan, Nigeria as the country introduces the rotavirus vaccine into its national immunization program.

Methods

Sixty-five stool samples were collected from children younger than 5 years with clinically diagnosed diarrhea and screened for the presence of rotavirus and norovirus using RT-PCR. Rotavirus-positive samples were further analyzed to determine the G and P genotypes using semi-nested multiplex PCR.

Results

The rates of rotavirus and norovirus positivity were 30.8% and 10.8%, respectively, whereas the rate of rotavirus and norovirus mixed infection was 4.6%. G1 was the predominant VP7 genotype, followed by G2, G9, and G1G2G9, whereas the predominant VP4 genotype was P[4], followed by P[6], P[8], and P[9]. The mixed P types P[4]P[8] and P[4]P[6] were also detected. G1P[4] was the most common VP4 and VP7 combination, followed by G2P[4], G1[P6], G1P[8], G2P[6], G2P[9], G9P[6], G2G9P[4], G2P[4]P[6], G1P[4]P[8], G2G9P[8], G1G2G9P[8], and G1[non-typable] P[non-typable], which were detected in at least 5% of the samples. Four samples had a combination of non-typable G and P types.

Conclusions

It is essential to monitor the circulation of virus strains prior to and during the implementation of the immunization program.

Human Bocavirus infection among children with respiratory tract infection in Ibadan, Nigeria

Background. Human Bocavirus (HBoV), which is an ssDNA virus of the family Parvoviridae, is responsible for 21.5 % of childhood respiratory tract infections (RTIs) annually. Among the four genotypes currently known, HBoV-1 has been associated with acute RTI. Although there have been studies on HBoV in some countries, there is limited information on this virus in sub-Saharan Africa where there is the highest burden of RTI. This study aimed to characterize the circulating strains of HBoV in Ibadan, Nigeria.

Methods. Nasopharyngeal and oropharyngeal swab samples were collected from 333 children ≤5 years old presenting with RTI attending hospitals in Ibadan, whose parents assented, from 2014 to 2015. Twenty-three HBoV isolates were sequenced after a nested PCR and phylogenetic analysis was carried out using mega 6 software.

Virological investigation of fatal rabies in a minor bitten by a mongrel in Nigeria

Rabies is a deadly viral disease transmitted through bites of infected animals. Outbreaks continue to escalate in Africa, with fatalities in humans, especially in rural areas, but are rarely reported. About 40% casualties occur among children of < 15 years. A 5-year-old boy on referral from a Primary Health Care Centre to a tertiary hospital presented with anxiety, confusion, agitation, hydrophobia, photo-phobia and aero-phobia, seven weeks after he was bitten by a stray dog in a rural community in Nigeria. The patient did not receive post-exposure prophylaxis and died 48 hours post admission. Confirmatory diagnosis was rabies and the phylogenetic analysis of the partial N-gene sequence of the virus localized it to Africa 2 (genotype 1) Lyssaviruses. There was 95.7-100% and 94.9-99.5% identity between the isolate and other genotype 1 Lyssaviruses and 100% homology with rabies viruses from Mali, Burkina Faso, Senegal and Central African Republic.

Adherence to Medication among Patients with Chronic Hepatitis B Infection Attending a Tertiary Hospital in South Western Nigeria

INTRODUCTION

Chronic hepatitis B (CHB) is an international public health problem. Treatment reduces its morbidity, mortality and infectivity. The aim of this study was to determine adherence among CHB infected patients on Tenofovir and the reasons for non-adherence.

METHODOLOGY

It was a cross-sectional study of patients on tenofovir for at least 6 months. Information was obtained on bio- data, adherence to tenofovir, duration and reasons for nonadherence using an interviewer administered questionnaire. Non- adherence was defined as patient reporting missing medication at all. Chi square or Fisher exact test and Student's t-test were used to determine associations. P value less than 0.05 was considered significant.

RESULTS

A total of 150 participants comprising of 76 (50.7%) females and 74 (49.3%) males with mean age of 39.2 ± 11.4 years, participated in the study. Non adherence rate was 65%. There was no significant association between non-adherence and tribe (p=0.7), level of education (p=0.8), religion (p=0.2), sex (p=0.9), clinical state (p=0.8), treatment experience (p=0.8) and months on Tenofovir (0.1) while a significant association existed with age (0.01), the presence of comorbidity (p=0.02) and taking another medication apart from tenfovir (0.00). The reasons for non-adherence included out of station 22 (14.7%), financial constraint 19(12.5%), unavailability of the drug 19 (12.5%), forgetfulness 15 (10%), perceived side effects 12 (8%), undetectable serum DNA quantification 11 (7.3%), ignorance of continuous use of Tenofovir 10 (6.7%), and pregnancy 9 (6%) among others.

CONCLUSION

Adherence to Tenofovir is poor among CHB patients attending University College Hospital, Ibadan.

Phylo-diversity of prevalent human E. coli O157:H7 with strains from retailed meat and fish in selected markets in Ibadan Nigeria

Global prevalence of ESBL-biotypes poses a serious threat to public health as a result of severity and morbidity caused by beta-lactam encoded Escherichia coli. Therefore, the prevalent shiga toxigenic Escherichia coli of ESBL variant was investigated in various retailed food animals and cooking materials. A total of 823 samples consisting of raw meat (297) and fish (132) samples retailed at various major markets in Ibadan were collected and 394 swabs were taken from the butchers' processing tables and utensils used in retailing meat and fish. The samples were cultured and biotyped for Escherichia coli. Serological and PCR assay were used to identify O157:H7 variant and antibiotics resistant determinants. Genetic relatedness of characterized E. coli O157 from human and meat products was evaluated with phylogenetic analysis. Of all the isolates, 130 (15.8%) were E. coli and only 8 (1.0) were O157:H7 while 4 (50%) were resistant to one or more antibiotics with resistance index ranging from 0.1 to 0.5. More than 25% E. coli O157:H7 were resistant to Ampicillin, Pefloxacin and Gentamicin and bla_SHV and bla_CTX-M were detected in 1/8 (12.5%) of E. coli O157:H7 and bla_TEM 3/8 (37.5%) respectively. Only 1 genotyped human Escherichia coli .0157:H7 clustered with beef strain There is evidence of blaTEM encoded E. coli O157:H7 causing infection in human from food animals retailed in many markets within various communities. Therefore, urgent surveillance with public health education, food, and environmental hygiene are highly needed to prevent its spread.

Phylogeography and evolutionary analysis of African Rotavirus a genotype G12 reveals district genetic diversification within lineage III

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.

Molecular characterization and evolutionary dynamics of measles virus sequences isolated from children in Lagos and Ibadan, South Western, Nigeria

Measles infection is endemic in Nigeria, with outbreaks occurring yearly. Genotype B3 is the dominant genotype and the only genotype characterized from Nigeria. The current study investigated the phylogenetic and Bayesian evolutionary dynamics of Nigerian measles virus Nucleoprotein (N) sequences isolated from Lagos and Ibadan, Nigeria. A total of 120 throat swab samples were analysed by RT-PCR and Sanger sequencing. Phylogenetic analysis and Bayesian demographic reconstructions were done using MEGA and BEAST software. Measles RNA positivity was 14.2% (17/120), age range 0-1 recorded the highest rate with 40.83%. Study sequences clustered within clade B3.1. The evolutionary rate of analysed B3 sequences was 1.108×10^-3, higher posterior density HPD interval (1.462×10^-3 - 7.886×10^-4)subs/site/year. The time to most recent common ancestor (T_MRC), was 1991. The Bayesian skyride analysis(BSP) of West African MV cladeB3.1, showed a stable, steady state population demography. This study has reemphasised the dominance of clade B3.1 in Nigeria. We have shown that clade B3.1 was recently introduced into circulation and has a slow population expansion. We advocate for the institution of molecular surveillance country wide in order to help monitor strain diversity and genetic evolution of Measles in Nigeria.

Epidemiology of Rotavirus A in Nigeria: Molecular Diversity and Current Insights

Rotavirus induced acute gastroenteritis AGE has been a major disease burden in Nigeria, since it was first reported in 1985. Prevalence rates have increased with severe public health consequences particularly among children. The vaccine Rotarix® has been introduced and is commercially available in Nigeria. However routine rotavirus vaccination is yet to be introduced into the National Immunization Program. Molecular epidemiology of rotavirus in Nigeria has shown the presence of various genotypes, with genotype G12P[8] being the most recent introduction. There are however gaps in molecular data on rotavirus in Nigeria. We therefore reviewed molecular data on rotavirus isolated in Nigeria and also analyzed VP4 and VP7 genes of Nigerian rotavirus strains in Genbank. We have shown that there is a distinct trend in rotavirus molecular epidemiology in Nigeria, with new genotype introductions occurring after the year 2010. We also observed from our analysis the emergence of genotype G12 Lineage III as a dominant genotype. This information elucidates rotavirus molecular epidemiology in Nigeria and gives insight to the expanding landscape of rotavirus genotypes. We recommend the institution of molecular surveillance country wide, before considering the inclusion of rotavirus vaccination into the National Immunization Program in Nigeria, in other to monitor evolution of divergent or recombinant strains.

Hepatitis B virus infection among sexually active individuals in Nigeria: a cross-sectional study

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.

Human Papilloma Virus Vaccine Awareness and Vaccination History in Patients Attending STI Clinics in Lagos and Ibadan, Nigeria

HPV is one of the most common causes of sexually transmitted disease in both men and women worldwide. It is transmitted through vaginal, anal, and oral sex. This study provided information on the Human Papilloma Virus (HPV) vaccine awareness and vaccination history in relation to the level of antibodies to (HPV) in the population at risk in Nigeria. Patients attending STI clinics at Lagos and Ibadan were recruited and informed consent was obtained from all the participants. Using semi structured questionnaire, vaccination history, demography and past experiences of the patients were obtained. Whole blood samples were obtained and the sera screened for specific antibodies to HPV using ELISA test kits for determination of IgG to HPV by DIA PRO Diagnostic Bioprobes Milano-Italy according to the manufacturer's instruction. Of the170 samples analysed 50 (29.4%) samples were positive for HPV. Thirty (17.6%) were from females and 20 (11.7%) of them were males. Thirty-five (35%) of the 100 women participants were aware of HPV vaccine. 15(15%) women did not take the vaccine because they did not know where to get it while 20 (20%) of them could not afford it. It was also noted that there is higher prevalence among the middle-aged women. A high prevalence of HPV antibodies was observed in the study yet none of the participants had received the HPV vaccine thus the antibodies may be from infection. Implication is that the 30 women who tested positive for the HPV antibodies may be at risk of cervical cancer.

FIRST MOLECULAR DETECTION AND VP7 (G) GENOTYPING OF GROUP A ROTAVIRUS BY SEMI-NESTED RT-PCR FROM SEWAGE IN NIGERIA

Rotavirus is the leading cause of viral gastroenteritis worldwide, and sewage is a major source of the virus dissemination in the environment. Our aim was to detect and genotype rotaviruses from sewages in Nigeria. One hundred and ninety sewage samples were collected between June 2014 and January 2015. The two phase concentration method using PEG 6000 and dextran was used to concentrate sewage samples following WHO protocols. Molecular detection was performed by RT-PCR, and VP7 genotyping by semi-nested multiplex PCR. A total of 14.2% (n = 27) samples tested positive. Monthly distribution showed that June to September had a lower rate (3.7% to 7.4%), while October to January recorded 11% to 26%. Genotype G1 predominated followed by G8, G9, G4 and lastly G2, 7.4% (n = 2) of isolates were nontypeable. This is the first report of rotavirus detection in sewages from Nigeria. Genotype G1 remains the most prevalent genotype. This observation calls for an effort by the governmental authorities to implement a molecular surveillance, both clinical and environmental, in order to provide vital information for the control and the vaccine efficacy not only in Nigeria, but globally.

Seasonal abundance and molecular identification of West Nile virus vectors, Culex pipens and Culex quinquefasciatus (diptera: culicidae) in Abeokuta, South-West, Nigeria

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.

Seroprevalence of transfusion transmissible infections (TTI), in first time blood donors in Abeokuta, Nigeria

BACKGROUND

Transfusion transmissible infections, such as HIV, HBV, HCV and syphilis are on the rise and pose a threat to blood safety.

OBJECTIVE

To determine prevalence and demographic profiles of TTI's among first time blood donors in Abeokuta, Nigeria.

METHODS

The study was conducted between February to November 2013; 130 first time blood donors were tested for the presence of HIV, HBsAg, HCV antibodies and Treponema palidium antibodies using EIA based rapid immunochromatographic kits. Data analysis was done using SPSS with a level of significance of p<0.05.

RESULTS

Prevalence rates to HIV, HBsAg, HCV antibody, were 6.2% (n=8), 10% (n=13) and 1.5% (n=2), there was 0% prevalence to Treponema palidium antibodies. Group specific prevalence rates revealed that educational status was associated with HBsAg positivity (p = 0.028), donors with a history of previous blood transfusion was also statistically associated with HIV sero-reactivity (p = 0.013).

CONCLUSIONS

High levels of HBsAg and HIV were observed, there is need to revise the donor testing algorithm in Nigeria in line with the prevalence of TTI's. We also advocate that a National surveillance system for TTI's be established through our National blood transfusion service (NBTS) program, a second serological test is also suggested to reduce the risk of occult HBV infection in Nigeria.