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.

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.

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.

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.

Polio virus neutralizing antibody dynamics among children in a north-central and South-Western Nigeria state.

Northern Nigeria accounts for the highest number of confirmed wild polio viruses globally. Transmission to neighboring countries is worrisome after the country failed to meet several deadlines for polio eradication. Most studies on neutralizing antibody have focused on the Northeastern and Northwestern regions. This study measured polio virus neutralizing antibody levels among children in North-central and South-western Nigeria. Children between the ages of 10 months and 13 yr were randomly selected from Abanishe-lolu Hospital Ilorin (North-central) and Oni Memorial and Adeoyo Hospitals in Ibadan (South-west) Nigeria. The alpha neutralization method was employed. Herd immunity was 1.4% in Ilorin, 36.6% in Oni Memorial Hospital, and 49.5% in Adeoyo Hospital. Out of 299 children studied, 49 (16.4%) children had no protection against all poliovirus serotypes while 100 (33.4%) were fully protected against all three serotypes. Five (7.9%) children in Ilorin and 5 (3.4%) children in Oni Memorial Hospital Ibadan had no detectable neutralizing antibody. A significant difference was observed (p=0.000) when the GMT against poliovirus 1, 2, and 3 was compared. A significant proportion of children were not fully protected. Sero-surveillance is recommended for effective monitoring of vaccination efforts to guide health policy formulators.

Kinetics of measles antibody by hemagglutination inhibition assay in children in south-west and north-central Nigeria.

OBJECTIVES: We investigated the antibody level of children against wild measles virus in view of recurrent measles epidemics, in order to provide information on immunization status for health policies and for the global measles mortality reduction initiative. METHODS: Two hundred and seventy-three children between the ages of 10 months and 13 years were recruited for this study from three hospital facilities in south-west and north-central Nigeria. Serum samples were collected from February to July 2009, and laboratory examination commenced in August of the same year. Measles hemagglutinin (HA) antigen was prepared by culturing the measles vaccine virus strain (Edmonston-Zagreb) in a vero/hSLAM cell line. Serum samples were treated to get rid of potentiating factors, non-specific inhibitors, and agglutinins before the HA/hemagglutination inhibition (HI) procedure. RESULTS: Out of the 175 children vaccinated in Ibadan, 60 (34.3%) had an antibody level not sufficient to protect against measles infection. Likewise, 12 (25.0%) vaccinated children from Ilorin had an antibody level not sufficient to protect against measles infection. There was no significant difference in the level of protection between the children in Ibadan and Ilorin (p>0.05). The geometric mean titer (GMT) was 53.83 for males and 48.64 for females. There was no significant difference between the GMTs of females and males in both locations (p>0.05). Also, no significant difference was observed in the GMTs of children in both locations (p>0.05). CONCLUSIONS: Of the vaccinated children, 157 (57.5%) developed protective measles virus HI antibody, which is not enough to maintain protective herd immunity. Hence there is a need for catch-up and follow-up vaccination programs, especially in rural areas and places with difficult terrains, in order to reduce measles mortality.