Molecular epidemiology and genetic evolution of avian influenza H5N1 subtype in Nigeria, 2006 to 2021.

Nigeria recorded one of the earliest outbreaks of the Highly Pathogenic Avian Influenza (HPAI) virus H5N1 in 2006, which spread to other African countries. In 2023, 18 countries reported outbreaks of H5N1 in poultry, with human cases documented in Egypt, Nigeria, and Djibouti. There is limited information on the molecular epidemiology of HPAI H5N1 in Nigeria. We determined the molecular epidemiology and genetic evolution of the virus from 2006 to 2021. We investigated the trend and geographical distribution across Nigeria. The evolutionary history of 61 full-length genomes was performed from 13 countries worldwide, and compared with sequences obtained from the early outbreaks in Nigeria up to 2021. MEGA 11 was used to determine the phylogenetic relationships of H5N1 strains, which revealed close ancestry between sequences in Nigeria and those from other African countries. Clade classification was performed using the subspecies classification tool for Bacterial and Viral Bioinformatics Research Center (BV-BRC) version 3.35.5. H5N1 Clade 2.2 was observed in 2006, with 2.3.2, 2.3.2.1f clades observed afterwards and 2.3.4.4b in 2021. Our findings underscore the need for genomics surveillance to track antigenic variation and clades switching to monitor the epidemiological of the virus and safeguard human and animal health.Impacts Specific variations in the hemagglutinin (HA) and neuraminidase (NA) genes of Avian influenza virus are consistent in different geographical regions. H5N1 Clade 2.2 was reported in 2006, with 2.3.2, 2.3.2.1f afterwards and 2.3.4.4b in 2021. Nigeria is an epicentre for avian influenza with three major migratory routes for wild birds transversing the country. It is plausible that the Avian influenza in Northern Nigeria may be linked to wild bird sanctuaries in the region.

Epidemiology of Human Mpox - Worldwide, 2018-2021.

Monkeypox (mpox) is a zoonotic disease caused by Monkeypox virus (MPXV), an Orthopoxvirus; the wild mammalian reservoir species is not known. There are two genetic clades of MPXV: clade I and clade II (historically found in central and west Africa, respectively), with only Cameroon reporting both clades (1). Human cases have historically been reported from 1) mostly rural, forested areas in some central and west African countries; 2) countries reporting cases related to population migration or travel of infected persons; and 3) exposure to imported infected mammals (2). The annual number of cases in Africa has risen since 2014 and cumulatively surpassed reports from the previous 40 years for most countries. This reemergence of mpox might be due to a combination of environmental and ecological changes, animal or human movement, the cessation of routine smallpox vaccination since its eradication in 1980, improvements in disease detection and diagnosis, and genetic changes in the virus (2). This report describes the epidemiology of mpox since 1970 and during 2018-2021, using data from national surveillance programs, World Health Organization (WHO) bulletins, and case reports, and addresses current diagnostic and treatment challenges in countries with endemic disease. During 2018-2021, human cases were recognized and confirmed in six African countries, with most detected in the Democratic Republic of the Congo (DRC) and Nigeria. The reemergence and increase in cases resulted in its being listed in 2019 as a priority disease for immediate and routine reporting through the Integrated Disease Surveillance and Response strategy in the WHO African region.* In eight instances, patients with mpox were identified in four countries outside of Africa after travel from Nigeria. Since 2018, introductory and intermediate training courses on prevention and control of mpox for public health and health care providers have been available online at OpenWHO.†,§ The global outbreak that began in May 2022¶ has further highlighted the need for improvements in laboratory-based surveillance and access to treatments and vaccines to prevent and contain the infection, including in areas of Africa with endemic mpox.

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.

Whole genome sequencing unravels cryptic circulation of divergent dengue virus lineages in the rainforest region of Nigeria.

Dengue is often misclassified and underreported in Africa due to inaccurate differential diagnoses of nonspecific febrile illnesses such as malaria, sparsity of diagnostic testing and poor clinical and genomic surveillance. There are limited reports on the seroprevalence and genetic diversity of dengue virus (DENV) in humans and vectors in Nigeria. In this study, we investigated the epidemiology and genetic diversity of dengue in the rainforest region of Nigeria. We screened 515 febrile patients who tested negative for malaria and typhoid fever in three hospitals in Oyo and Ekiti States in southern Nigeria with a combination of anti-dengue IgG/IgM/NS1 rapid test kits and metagenomic sequencing. We found that approximately 28% of screened patients had previous DENV exposure, with the highest prevalence in persons over sixty. Approximately 8% of the patients showed evidence of recent or current infection, and 2.7% had acute infection. Following sequencing of sixty samples, we assembled twenty DENV-1 genomes (3 complete and 17 partial). We found that all assembled genomes belonged to DENV-1 genotype III. Our phylogenetic analyses showed evidence of prolonged cryptic circulation of divergent DENV lineages in Oyo state. We were unable to resolve the source of DENV in Nigeria owing to limited sequencing data from the region. However, our sequences clustered closely with sequences in Tanzania and sequences reported in Chinese with travel history to Tanzania in 2019. This may reflect the wider unsampled bidirectional transmission of DENV-1 in Africa, which strongly emphasizes the importance of genomic surveillance in monitoring ongoing DENV transmission in Africa.

Metagenomic Detection and Genetic Characterization of Human Sapoviruses among Children with Acute Flaccid Paralysis in Nigeria.

Using a metagenomic sequencing approach on stool samples from children with Acute Flaccid Paralysis (AFP), we describe the genetic diversity of Sapoviruses (SaVs) in children in Nigeria. We identified six complete genome sequences and two partial genome sequences. Several SaV genogroups and genotypes were detected, including GII (GII.4 and GII.8), GIV (GIV.1), and GI (GI.2 and GI.7). To our knowledge, this is the first description of SaV infections and complete genomes from Nigeria. Pairwise identity and phylogenetic analysis showed that the Nigerian SaVs were related to previously documented gastroenteritis outbreaks with associated strains from China and Japan. Minor variations in the functional motifs of the nonstructural proteins NS3 and NS5 were seen in the Nigerian strains. To adequately understand the effect of such amino acid changes, a better understanding of the biological function of these proteins is vital. The identification of distinct SaVs reinforces the need for robust surveillance in acute gastroenteritis (AGE) and non-AGE cohorts to better understand SaVs genotype diversity, evolution, and its role in disease burden in Nigeria. Future studies in different populations are, therefore, recommended.

Changing Ecotypes of Dengue Virus 2 Serotype in Nigeria and the Emergence of Cosmopolitan and Asian I Lineages, 1966-2019.

Dengue virus (DENV) is a leading mosquito-borne virus with a wide geographical spread and a major public health concern. DENV serotype 1 (DENV-1) and serotype 2 (DENV-2) were first reported in Africa in 1964 in Ibadan, Nigeria. Although the burden of dengue is unknown in many African countries, DENV-2 is responsible for major epidemics. In this study, we investigated the activities of DENV-2 to determine the circulating strains and to appraise the changing dynamics in the epidemiology of the virus in Nigeria. Nineteen DENV-2 sequences from 1966-2019 in Nigeria were retrieved from the GenBank of the National Center of Biotechnology Information (NCBI). A DENV genotyping tool was used to identify the specific genotypes. The evolutionary history procedure was performed on 54 DENV-2 sequences using MEGA 7. There is a deviation from Sylvatic DENV-2 to other genotypes in Nigeria. In 2019, the Asian I genotype of DENV-2 was predominant in southern Edo State, located in the tropical rainforest region, with the first report of the DENV-2 Cosmopolitan strain. We confirmed the circulation of other non-assigned genotypes of DENV-2 in Nigeria. Collectively, this shows that DENV-2 dynamics have changed from Sylvatic transmission reported in the 1960s with the identification of the Cosmopolitan strain and Asian lineages. Sustained surveillance, including vectorial studies, is required to fully establish the trend and determine the role of these vectors.

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.

Detection of Hepatitis B Surface Antigen among Febrile Patients in Ankpa, Kogi State, Nigeria.

BACKGROUND: Hepatitis B virus (HBV) infection has become a significant public health problem in developing countries, and the high rate of morbidity and mortality from acute and chronic infections is worrisome. Therefore, this study determined the prevalence of HBV and associated risk factors in Ankpa, Kogi State, Nigeria. Materials and Methods. Sera randomly collected from 200 participants in three public hospitals in Ankpa were screened for HBsAg using commercially available HBsAg rapid test kit (Swe-Care (R), China). Structured questionnaires were used to obtain sociodemographic details and history of exposure to risk factors. RESULTS: Seventeen (8.5%) of the 200 patients were positive for HBsAg. Males had higher prevalence (10.89%) than females (6.06%). The age group with the highest rate of infection was 24-44 years. Patient's occupation and marital status were significantly higher in relation to HBsAg seropositivity. Risks of HBV infection in Ankpa are sharing of sharp objects (OR = 11.62, 95% CI, 3.59-37.59), multiple sexual partners (OR = 3.39, 95% CI, 1.23-9.38), blood transfusion (OR = 13.74, 95% CI, 4.22-44.71), surgeries (OR = 3.02, 95% CI, 1.03-8.83), alcoholism (OR = 6.94, 95% CI, 2.32-20.75), mouth-to-mouth kissing (p=0.001), and contact with HBV patient (OR = 4.14, 95% CI, 1.01-17.06). People without prior knowledge of HBV infection were more infected. CONCLUSION: This study reaffirms the endemicity of HBV in a part of sub-Saharan African country. Public health practitioners should focus attention on apparently healthy patients in developing countries. We suggest inclusion of HBsAg screening for patients coming for routine hospital care.

Seroprevalence of chikungunya virus infection in five hospitals within Anyigba, Kogi State of Nigeria.

Febrile illnesses in developing countries are often misdiagnosed as malaria or typhoid fever. Although arboviral infections have similar clinical symptoms, they are usually not screened because of limited resources and the fact that there are several viruses in this group. Chikungunya virus (CHIKV) has been isolated in parts of Nigeria, but there is no documented evidence of the infection in Kogi State. This study determined seroprevalence of active and past CHIKV infection among febrile patients who tested negative for malaria and typhoid fever. Sera from 243 febrile patients were screened for CHIKV IgG and IgM using an immunochromatographic test kit. Clinical and socio-demographic variables were collected using a structured questionnaire. Recent CHIKV infection was observed in 5.8% of the study participants while 25.1% had IgG antibodies demonstrating previous infection. Significant associations were observed between seropositivity and age of participants (p<0.001), sex (p=0.044), marital status (p=0.002), and occupation (p<0.001). Clinical symptoms such as fever, joint pain, and headache were significantly associated with seropositivity. This study identified recent CHIKV infection in Anyigba. Therefore, there is need for routine screening of febrile patients and molecular characterization to determine the nature of circulating strains.

Knowledge, attitude and practice of medical laboratory practitioners in the fight against Ebola virus disease.

INTRODUCTION: Ebola virus disease (EVD) in West Africa was an enormous public health challenge. Nigeria was able to contain the spread of the virus with a concerted effort and an effective public health response in terms of identification of contacts, rapid laboratory diagnosis, quarantine and symptomatic treatment. We determined the knowledge, attitude and practice of medical laboratory practitioners (MLPs) in this post-Ebola epidemic era. METHODS: This cross-sectional study was carried out in eight hospitals in Kano State for 6 months, between January and June 2016. It involved medical laboratory scientists (MLS), medical laboratory technicians (MLT) and medical laboratory assistants (MLA). Questionnaires were administered and analysed. RESULTS: Of the 75 participants, mean knowledge score was 5.54 (standard deviation [SD] ±1.44) while the mean attitude score was 13.72 ±2.80, and mean practice score was 3.10 ±0.80. Mean age of participants was 36.82 ± 8.07 years. There was full awareness of EVD among all 75 participants; however, many medical laboratory practitioners (52.7%) did not know EVD prevention methods. The majority (86.1%) knew the source of disease outbreak and most MLPs (66.7%) practised improper hand washing to prevent Ebola transmission. In addition, they had a negative attitude and practice towards EVD. Of 71 MLPs, 52 (73.2%) strongly disagreed that a traditional remedy was preferable in EVD treatment. CONCLUSION: Fear of EVD among MLPs has declined.

High Rate of Hepatitis B Virus Surface Antigenemia Among People Living with HIV/AIDS in Kakuri, Kaduna State, North West Nigeria.

Globally, increased incidence of liver disease caused by hepatitis B virus (HBV) is responsible for high morbidity and mortality among human immunodeficiency virus (HIV)-infected individuals. This is because both viruses share common routes of transmission. We determined prevalence of HBV-HIV coinfection and the influence of some risk factors on concomitant infection among people living with HIV in a treatment center in Kakuri, Kaduna State. Two hundred consenting individuals with HIV infection participated in the study. Fifty-seven males and 143 females were screened using commercial hepatitis B virus surface antigen (HBsAg) rapid membrane-based immunoassay kit (Fastep™ HBV). Seventeen patients tested positive to HBsAg (8.5%). There were more males (14.0%) than females (6.3%). Patients within 40-49 years of age had more coinfection (20.6%) compared to those older than 50 years who had the least prevalence (2.7%). Age of HBV/HIV coinfection was statistically significant (p = 0.02). Risk factors include no knowledge of HBV infection, sharing sharp objects, history of sexually transmitted diseases, history of surgeries, and no HBV immunization. High infection rate observed in this study underscores the need for public awareness, to educate people on modes of transmission. Routine screening is advocated for early HBV identification, as this will facilitate reduction of comorbidity and mortality resulting from opportunistic infection. Findings from this study support introduction of HBV vaccination as part of the Expanded Programme on Immunization in Nigeria.

Status of Laboratory Biosafety and Biosecurity in Veterinary Research Facilities in Nigeria.

BACKGROUND: This study determined current status of laboratory biosafety in Nigerian veterinary research facilities. METHODS: A questionnaire was developed to obtain information from researchers across Nigeria from July 2014 to July 2015. Information regarding demographics, knowledge of laboratory biosafety, availability and proper use of personal protective equipment (PPE), any priority pathogens researched, attitude on and use of standard laboratory practices, and biosafety awareness was obtained using a numeric scoring system. Data were analyzed with descriptive statistics, and univariate and multivariate logistic regression. RESULTS: A total of 74 participants from 19 facilities completed the questionnaire. General knowledge scores ranged from 3 to 28 (out of 28 possible points), with 94.6% of respondents receiving low scores (scores < mean + 1 standard deviation). Very few (17.6%) reported availability or use PPE. Many participants (63.5%) reported no access to biosafety level (BSL)-1-3 facilities. None reported availability of a BSL-4 facility. Knowledge scores pertaining to biosafety management practices ranged from 0 to 14 (out of 14 possible points) with 47.3% of respondents receiving good scores (scores > mean + 1 standard deviation). Only 16.2% of respondents (from four facilities) reported having biosafety officers. Rabies virus was the most researched pathogen (31.1% of respondents). The majority (71.6%) were unaware of laws guiding biosafety. Researchers [odds ratio (OR) = 18.0; 95% confidence interval (CI): 1.63, 198.5; p = 0.023], especially in BSL-2 (OR = 258.5; 95% CI: 12.71, 5256; p < 0.001) facility of research institute (OR = 25.0; 95% CI: 5.18, 120.6; p < 0.001), are more likely to have adequate access to and properly utilize biosafety devices and PPE. CONCLUSIONS: Current knowledge of laboratory biosafety is limited except among a few researchers.

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 chikungunya virus infection in five hospitals within Anyigba, Kogi State of Nigeria

ABSTRACT Febrile illnesses in developing countries are often misdiagnosed as malaria or typhoid fever. Although arboviral infections have similar clinical symptoms, they are usually not screened because of limited resources and the fact that there are several viruses in this group. Chikungunya virus (CHIKV) has been isolated in parts of Nigeria, but there is no documented evidence of the infection in Kogi State. This study determined seroprevalence of active and past CHIKV infection among febrile patients who tested negative for malaria and typhoid fever. Sera from 243 febrile patients were screened for CHIKV IgG and IgM using an immunochromatographic test kit. Clinical and socio-demographic variables were collected using a structured questionnaire. Recent CHIKV infection was observed in 5.8% of the study participants while 25.1% had IgG antibodies demonstrating previous infection. Significant associations were observed between seropositivity and age of participants (p < 0.001), sex (p = 0.044), marital status (p = 0.002), and occupation (p < 0.001). Clinical symptoms such as fever, joint pain, and headache were significantly associated with seropositivity. This study identified recent CHIKV infection in Anyigba. Therefore, there is need for routine screening of febrile patients and molecular characterization to determine the nature of circulating strains.

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.