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Abstract Multivalent antigen display is a fast-growing area of interest toward broadly protective vaccines. Current nanoparticle-based vaccine candidates demonstrate the ability to confer antibody-mediated immunity against divergent strains of notably mutable viruses. In coronaviruses, this work is predominantly aimed at targeting conserved epitopes of the receptor binding domain. However, targeting conserved non-RBD epitopes could limit the potential for antigenic escape. To explore new potential targets, we engineered protein nanoparticles displaying coronavirus prefusion-stabilized spike (CoV_S-2P) trimers derived from MERS-CoV, SARS-CoV-1, SARS-CoV-2, hCoV-HKU1, and hCoV-OC43 and assessed their immunogenicity in female mice. Monotypic SARS-1 nanoparticles elicit cross-neutralizing antibodies against MERS-CoV and protect against MERS-CoV challenge. MERS and SARS nanoparticles elicit S1-focused antibodies, revealing a conserved site on the S N-terminal domain. Moreover, mosaic nanoparticles co-displaying distinct CoV_S-2P trimers elicit antibody responses to distant cross-group antigens and protect male and female mice against MERS-CoV challenge. Our findings will inform further efforts toward the development of pan-coronavirus vaccines.

Summary: Immunogen design approaches aim to control the specificity and quality of antibody responses elicited by next-generation vaccines. Here, we use computational protein design to generate a nanoparticle vaccine platform based on the receptor-binding domain (RBD) of influenza hemagglutinin (HA) that enables precise control of antigen conformation and spacing. HA RBDs are presented as either monomers or native-like closed trimers that are connected to the underlying nanoparticle by a rigid linker that is modularly extended to precisely control antigen spacing. Nanoparticle immunogens with decreased spacing between trimeric RBDs elicit antibodies with improved hemagglutination inhibition and neutralization potency as well as binding breadth across diverse H1 HAs. Our “trihead” nanoparticle immunogen platform provides insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used in next-generation vaccines against influenza and other viruses.

Two-component, self-assembling nanoparticles represent a versatile platform for multivalent presentation of viral antigens. Computational design of protein nanoparticles with differing sizes and geometries enables combination with antigens of choice to test novel multimerization concepts in immunization strategies where the goal is to improve the induction and maturation of neutralizing antibody lineages. Here, we describe detailed antigenic, structural, and functional characterization of computationally designed tetrahedral, octahedral, and icosahedral nanoparticle immunogens displaying trimeric HIV envelope glycoprotein (Env) ectodomains. Env trimers, based on subtype A (BG505) or consensus group M (ConM) sequences and engineered with SOSIP stabilizing mutations, were fused to an underlying trimeric building block of each nanoparticle. Initial screening yielded one icosahedral and two tetrahedral nanoparticle candidates, capable of presenting twenty or four copies of the Env trimer. A number of analyses, including detailed structural characterization by cryo-EM, demonstrated that the nanoparticle immunogens possessed the intended structural and antigenic properties. When the immunogenicity of ConM-SOSIP trimers presented on a two-component tetrahedral nanoparticle or as soluble proteins were compared in rabbits, the two immunogens elicited similar serum antibody binding titers against the trimer component. Neutralizing antibody titers were slightly elevated in the animals given the nanoparticle immunogen and were initially more focused to the trimer apex. Altogether, our findings indicate that tetrahedral nanoparticles can be successfully applied for presentation of HIV Env trimer immunogens; however, the optimal implementation to different immunization strategies remains to be determined.

Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self-assembling protein nanoparticles with geometries tailored to present the ectodomains of influenza, HIV, and RSV viral glycoprotein trimers. We first de novo designed trimers tailored for antigen fusion, featuring N-terminal helices positioned to match the C termini of the viral glycoproteins. Trimers that experimentally adopted their designed configurations were incorporated as components of tetrahedral, octahedral, and icosahedral nanoparticles, which were characterized by cryo-electron microscopy and assessed for their ability to present viral glycoproteins. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles presented antigenically intact prefusion HIV-1 Env, influenza hemagglutinin, and RSV F trimers in the predicted geometries. This work demonstrates that antigen-displaying protein nanoparticles can be designed from scratch, and provides a systematic way to investigate the influence of antigen presentation geometry on the immune response to vaccination.

OBJECTIVES/GOALS: Lack of blood vessels remains a major obstacle in tissue regeneration. Angiopoietin 1 and 2 modulate angiogenesis through the Tie2 receptor tyrosine kinase. Ang1 activates pAKT to promote endothelial cell survival while Ang2 antagonizes these effects. We aim to dissect the Ang/Tie2 pathway to uncover the molecular basis for these opposing effects. METHODS/STUDY POPULATION: Ang1 and Ang2 bind Tie2 via nearly identical F-domains (Fd). To investigate the molecular basis regulating the Tie2 pathway, we generated a series of computationally designed self-assembling protein scaffolds presenting F-domains in a wide range of valencies and geometries using Rosette Molecular Modeling Suite. We examined the protein kinase activation, cell migration, and blood vessel formation produced by the designed proteins in human umbilical vein endothelial cells. RESULTS/ANTICIPATED RESULTS: Two phenotypic classes were demonstrated by the number of presented F domains: scaffolds presenting 3 or 4 Fd have Ang2 like activity, upregulating pFAK and pERK but not pAKT and failing to induce cell migration and tube formation; scaffolds presenting more than 6 Fd have Ang1 like activity, upregulating the three signaling branches and enhancing cell migration and tube formation. Scaffolds with 8 or more Fd show superagonist activity, producing significantly stronger phenotypes than Ang1. These results suggest that Fd valency largely determines Ang1 vs Ang2 signaling outcomes, and our designed superagonists can outperform Ang1 in vascularization and wound healing. In in vivo experiments, nanoparticles displaying 60 copies of Fd produce significant revascularization in hemorrhagic brains. DISCUSSION/SIGNIFICANCE OF IMPACT: Targeting the Tie2 pathway is a new paradigm in regenerative medicine. Our designed constructs will enable us to generate high-affinity Tie2 agonists and antagonists as drugs to control angiogenesis, enabling tissue regeneration that recapitulates the biological architecture of the native tissue physiology, improving organ transplant outcome.

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.

Bats are not only ecologically valuable mammals but also reservoirs of zoonotic pathogens. Their vast population, ability to fly, and inhabit diverse ecological niches could play some role in the spread of antibiotic resistance. This study investigated non-aureus staphylococci and Mammaliicoccus colonization in the Hipposideros bats at Obafemi Awolowo University, Ile-Ife, Nigeria. Pharyngeal samples (n = 23) of the insectivorous bats were analyzed, and the presumptive non-aureus staphylococcal and Mammaliicoccus isolates were confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The isolates were characterized based on antibiotic susceptibility testing and whole-genome sequencing (WGS). Six bacterial genomes were assembled, and three species were identified, including Mammaliicoccus sciuri (n = 4), Staphylococcus gallinarum (n = 1), and Staphylococcus nepalensis (n = 1). All the isolates were resistant to clindamycin, while the M. sciuri and S. gallinarum isolates were also resistant to fusidic acid. WGS analysis revealed that the M. sciuri and S. gallinarum isolates were mecA-positive. In addition, the M. sciuri isolates possessed some virulence (icaA, icaB, icaC, and sspA) genes. Multi-locus sequence typing identified two new M. sciuri sequence types (STs) 233 and ST234. The identification of these new STs in a migratory mammal deserves close monitoring because previously known ST57, ST60, and ST65 sharing ack (8), ftsZ (13), glpK (14), gmk (6), and tpiA (10) alleles with ST233 and ST234 have been linked to mastitis in animals. Moreover, the broad host range of M. sciuri could facilitate the dispersal of antibiotic resistance genes. This study provides evidence of the importance of including migratory animals in monitoring the development and spread of antibiotic resistance., (© 2024. The Author(s).)

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.

Since SARS-CoV-2 caused the COVID-19 pandemic, records have suggested the occurrence of reverse zoonosis of pets and farm animals in contact with SARS-CoV-2-positive humans in the Occident. However, there is little information on the spread of the virus among animals in contact with humans in Africa. Therefore, this study aimed to investigate the occurrence of SARS-CoV-2 in various animals in Nigeria. Overall, 791 animals from Ebonyi, Ogun, Ondo, and Oyo States, Nigeria were screened for SARS-CoV-2 using RT-qPCR ( n = 364) and IgG ELISA ( n = 654). SARS-CoV-2 positivity rates were 45.9% (RT-qPCR) and 1.4% (ELISA). SARS-CoV-2 RNA was detected in almost all animal taxa and sampling locations except Oyo State. SARS-CoV-2 IgGs were detected only in goats from Ebonyi and pigs from Ogun States. Overall, SARS-CoV-2 infectivity rates were higher in 2021 than in 2022. Our study highlights the ability of the virus to infect various animals. It presents the first report of natural SARS-CoV-2 infection in poultry, pigs, domestic ruminants, and lizards. The close human-animal interactions in these settings suggest ongoing reverse zoonosis, highlighting the role of behavioral factors of transmission and the potential for SARS-CoV-2 to spread among animals. These underscore the importance of continuous monitoring to detect and intervene in any eventual upsurge.

Infection with both Hepatitis B (HBV) and D (HDV) virus causes more severe liver damage than HBV alone. Superinfections among chronic HBV infected cohorts often lead to HDV persistence with rapid progression to cirrhosis, necessitating continuous surveillance to determine their prevalence and relative contribution to liver pathology. A cross-sectional study among hospital outpatients in Ekiti and Osunstates was conducted using random sampling technique. Blood samples were collected from 410 participants and tested for HBV serological markers. All samples positive for HBsAg samples were tested for Hepatitis D virus antigen (HDAg), serum anti-HDV IgM, and serum anti-HDV IgG using enzyme-linked immunosorbent assay kits. The prevalence of HBV infection among the 410 samples was 12.4% (CI 9.5-15.9). Past HBV exposure was detected in 120 (29.2%), while 147(35.8%) were susceptible to HBV infection. Among the HBsAg positive individuals, 9.8% were hepatitis D antigen (HDAg) positive, while 3.9% and 1.9% were positive for IgG anti-HDV and IgM anti-HDV, respectively. Risk factors associated with HBV infections in this study were multiple sexual partners and sharing of sharp objects. Our investigation has verified the endemicity of HBV in Nigeria and revealed that HBV- HDV co-infection is highly prevalent in south-west Nigeria.

Hepatitis B virus (HBV) infection follows a natural course of events predicted by a dynamic interaction between viral antigen and the host immune system, which forms the basis for HBV serological diagnosis. These interactions may deviate from the typical serologic patterns. This study investigates the types of atypical HBV serologic profiles (AHBSP) across clinical cohorts of patients with HBV infection in southwestern Nigeria. This is a cross-sectional, hospital-based, multi-centered study. Patients' sera were analyzed for HBsAg, anti-HBs, HBeAg, anti-HBe, anti-HBc IgM, and anti-HBc IgG by ELISA from 279 study participants attending selected gastroenterology clinics between August 2019 and December 2020. The prevalence of atypical HBV serologic profiles was 27% (n = 76). The mean age of patients was 35.7 ± 11.2 years. The gender distribution involved 183 females (65.6%) and 96 males (34.4%). Across clinical cohorts of patients with atypical serologic profiles, HBeAg Negative, anti-HBe positive with detectable HBV DNA had the highest prevalence of 21% followed by isolated anti-HBc antibody positive, HBsAg negative and detectable HBV DNA, 5%. The atypical serologic profiles, HBeAg positive, HBsAg negative with detectable HBV DNA and concurrent anti-HBs with HBsAg, had the lowest prevalence, 0.4%, respectively. This study identified the considerable presence of atypical HBV serologic profiles across clinical cohorts of HBV infection in southwestern Nigeria.

Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates., (© 2023. The Author(s).)

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Mosquito vectors are a tremendous public health threat. One in six diseases worldwide is vector-borne transmitted mainly by mosquitoes. In the last couple of years, there have been active Yellow fever virus (YFV) outbreaks in many settings in Nigeria, and nationwide, entomological surveillance has been a significant effort geared towards understanding these outbreaks. In this study, we used a metagenomic sequencing approach to characterize viruses present in vector samples collected during various outbreaks of Yellow fever (YF) in Nigeria between 2017 and 2020. Mosquito samples were grouped into pools of 1 to 50 mosquitoes, each based on species, sex and location. Twenty-five pools of Aedes spp and one pool of Anopheles spp collected from nine states were sequenced and metagenomic analysis was carried out. We identified a wide diversity of viruses belonging to various families in this sample set. Seven different viruses detected included: Fako virus, Phasi Charoen-like virus, Verdadero virus, Chaq like-virus, Aedes aegypti totivirus, cell fusing agent virus and Tesano Aedes virus. Although there are no reports of these viruses being pathogenic, they are an understudied group in the same families and closely related to known pathogenic arboviruses. Our study highlights the power of next generation sequencing in identifying Insect specific viruses (ISVs), and provide insight into mosquito vectors virome in Nigeria., (© 2022. The Author(s).)

Introduction: Hepatitis B virus (HBV) infection continues to be a significant public health challenge globally, with higher disease burden in developing countries. HBV genotypes are associated with different geographical regions and clinical outcomes. Limited information exists on epidemiology of HBV in the Niger-Delta region (South-South) of Nigeria. Consequently, this study was designed to characterise hepatitis B virus infection among outpatients in selected tertiary hospitals in the region., Methodology: Between June and August 2017, consenting nine hundred asymptomatic out-patients were enrolled and initially screened for HBV infection using one step Hepatitis B surface antigen (HBsAg) strip and subsequently re-tested using HBsAg and Hepatitis B core total antibody (anti-HBc) specific Enzyme-Linked Immunosorbent Assay (ELISA). Blood serum with detectable HBsAg were subsequently subjected to DNA extraction, S-gene amplification using a nested polymerase chain reaction (PCR) protocol, gel electrophoresis, sequencing and phylogenetic analysis., Results: Seroprevalence of HBsAg was 4.6% (95% CI 2.5-7.1) and anti-HBc was 10.1% (95% confidence interval (CI) 6.1-15.3). Of the 41 HBsAg positive samples subjected to DNA extraction and HBV S-gene specific PCR, only 6 (14.6%) yielded the expected ∼408bp band. Phylogenetic analysis based on HBV pre-S/S sequences identified all six typable samples as genotype E, subtype ayw4 of the West African clade., Conclusion: Results of the study confirm the presence and circulation of HBV genotype-E in the Niger-Delta region of Nigeria, thus corroborating the inclusion of the country in the Genotype E crescent. The authors advocate value-added HBV intervention in the region and the country at large., (© 2022 Umego CF et al.)

Outbreaks of infectious bursal disease (IBD), a highly contagious immunosuppressive disease of young chickens, are still reported globally despite vaccination efforts. This study investigated the genetic characteristics of infectious bursal disease virus (IBDV) from 26 reported outbreaks in 2019 in Nigeria. Nucleotide sequences of VP2 hypervariable (hvVP2) region (n=26) and VP1 (n=23) of Nigerian IBDVs were determined. Our results revealed the detection of reassortant strains with segment A related to very virulent IBDV (vvIBDV) having virulence marker (222A, 242I, 256I, 294I and 299S), whereas their segment B were closely related to previously detected IBDV strains having QEG substitution at positions 145-147. Phylogenetic analysis of the hvVP2 region revealed that all the Nigerian IBDV clustered with vvIBDV (genogroup 3) and were independent of the Asian/European lineage. Interestingly, in the hvVP2, all the viruses had a G-S substitution at residue 254. Additionally, one isolate had an A321T substitution at the P HI loop, which has been suggested to play a key role in antigenicity. Four of the viruses (Bauchi=3 and Plateau=1) had a unique A-T substitution at residue 144 on the VP1 region. We also observed a T174S substitution in nine of the Nigerian viruses from Bauchi and Plateau state that were not found in any outbreak viruses from Oyo and Akwa Ibom. This report demonstrates the circulation of reassortant strains in commercial and backyard poultry farms in Nigeria despite sustained vaccination efforts. Our data suggest that the Nigerian outbreak viruses have mutations that may affect antigenicity and contribute to antigenic drift.

Introduction. Hepatitis B virus (HBV) infection is the leading cause of hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). HBV genotype E (HBV/E) is the predominant genotype in West Africa and has been linked epidemiologically with chronic and occult HBV infections as well as development of HCC. Mutations in the surface and polymerase genes of HBV have been associated with occult infection, drug resistance, vaccine escape, as well as HCC. Hypothesis/Gap Statement. There is limited data on the occurrence and patterns of mutations associated with occult infection, drug resistance, vaccine escape and HCC for HBV/E. Aim. This study characterized amino acid (aa) substitutions in the major hydrophilic (MHR) and reverse transcriptase (RT) regions of the surface and polymerase genes respectively of HBV sequences from a group of Nigerians with genotype E infection. The CpG islands of the PreC/C and PreS/S regions of these sequences were also described. Methodology. HBV surface and polymerase genes were detected using PCR techniques. Occurrence of new and previously described mutations in these genes were analysed using phylogenetic techniques. Results. Overall 13 HBV isolates were each sequenced for polymerase and surface genes mutations. Thirteen and nine PreS/S and PreC/C HBV genes respectively were analysed for CpG islands. Mutations in the MHR and a-determinants region of the S protein were discovered in eleven and nine of the 13 tested isolates respectively. These mutations were concomitant with aa changes in the RT functional domains of the isolates. Mutations associated with vaccine escape, occult infection and poor HCC prognosis were identified in HBV/E isolated in this study. Furthermore, all the isolates had at least one putative nucleotide analogue resistance mutations. Drug resistance mutations had the highest association with CpG islands. Conclusion. The results of this study contribute to further understanding of HBV variability in Nigeria and the West African region. This will aid the planning of adequate HBV immunization and treatment programmes for the countries in the region.

We recently investigated the presence of enteroviruses (EVs) in non-human primates (NHPs) in Northern Nigeria and documented the presence of EV-A76 of South-East Asian ancestry in an NHP. In this study, we go further to ask if we could also find EVs in NHPs indigenous to the forested South-south Nigeria. Fresh faecal samples were collected from the floor of 10 cages housing NHPs in Cross River Nigeria, re-suspended in PBS and subjected to RNA extraction, cDNA synthesis, PanEnt 5'-UTR and PanEnt VP1 PCR assays. None of the samples was positive for the PanEnt VP1 assay, but one sample was positive for PanEnt 5'-UTR PCR. This sample was subsequently inoculated into RD cell line, produced CPE and the isolate analysed by PCR assays, next-generation whole genome sequencing and passage in four different cell lines showing replication in two of them. Analysis of the complete genome of the isolate identified it as an Echovirus 11 (E11) and revealed a recombinant genomic structure. Phylogenetic analysis showed that the E11 NHP strain was related to human clinical isolates suggesting a zoonotic behaviour. We describe the first isolation and complete genome characterization of an E11 obtained from an NHP in Nigeria having zoonotic potential.

Effective disease outbreak response has historically been a challenging accomplishment for the Nigerian health system due to an array of hurdles not unique to Nigeria but also found in other African nations which share its large size and complexity. However, the efficiency of the response mounted against the Ebola Virus Disease (EVD) outbreak of 2014 proved that indeed, though challenging, proactive and effective outbreak response is not impossible. With over 20 public health emergencies and infectious disease outbreaks between 2016 and 2018 alone, Nigeria is one of only five members of the World Health Organization (WHO) African Region to report five or more public health events per annum. There are many lessons that can be drawn from Nigeria's experience in handling outbreaks of infectious diseases. In this review, we discuss the history of emerging and re-emerging infectious disease outbreaks in Nigeria and explore the response strategies mounted towards each. We also highlight the significant successes and note-worthy limitations, which we have then utilized to proffer policy recommendations to strengthen the Nigerian public health emergency response systems., Competing Interests: Conflict of interest: All authors declare no conflicts of interest in this paper., (© 2020 the Author(s), licensee AIMS Press.)

Here, we describe the near-complete genome of an enterovirus F (EV-F) isolate from Nigeria. The obtained sequence was 7,378 nucleotides (nt) long and encodes 2 open reading frames (ORFs), an upstream ORF (uORF; 56 amino acids [aa]) and a polyprotein ORF (ppORF; 2,167 aa). Both ORFs overlap but are in different reading frames, with the uORF in a +1 reading frame relative to the ppORF., (Copyright © 2020 Faleye et al.)

In 2018, a 26-month-old girl, fully vaccinated with Rotarix in 2016, presented with fever, diarrhea, and vomiting. A rapid test showed that her feces contained rotavirus A (RVA). VP7 reverse transcription-PCR (RT-PCR) and Illumina sequencing showed that a G1P[8] strain with a Wa-like genotype constellation was the etiologic agent. This is the first near-complete RVA genome sequence from Nigeria., (Copyright © 2020 Faleye et al.)

We describe the draft genome of a bovine enterovirus (EV) isolate recovered from sewage in Nigeria. This isolate replicates on both RD and L20B cell lines but is negative for all EV screens in use by the Global Poliovirus Eradication Initiative (GPEI). It contains 7,368 nucleotides (nt) with 50.2% G+C content and an open reading frame (ORF) with 6,525 nt (2,174 amino acids).

We present the draft genome of Mycoplasma arginini strain NGR_2017. This strain was recovered in Nigeria from cell culture in 2017. The assembly contains 620,555 bp in 12 contigs. It contains 561 coding sequences, 34 RNAs (29 tRNAs, 4 rRNAs, and 1 transfer-messenger RNA [tmRNA]), and a >26-kb integrative and conjugative element., (Copyright © 2018 Adeniji et al.)

Recently, a reverse transcriptase semi-nested polymerase chain reaction (RT-snPCR) assay was recommended by the WHO for direct detection of enteroviruses in clinical specimens. In this study, we use this assay and a modification thereof to screen acute flaccid paralysis (AFP) samples that had previously tested negative for enteroviruses by the RD-L20B algorithm. Thirty paired stool suspensions collected in 2015 as part of the national AFP surveillance program in different states of Nigeria were analyzed in this study. The samples had previously tested negative for enteroviruses in the polio laboratory in accordance with the WHO-recommended RD-L20B-cell-culture-based algorithm. Two samples that had previously been found to contain enteroviruses were included as positive controls. All samples were subjected to RNA extraction, the RT-snPCR assay and a modified version of the RT-snPCR. All amplicons were sequenced, and enteroviruses were identified using the enterovirus genotyping tool and phylogenetic analysis. Amplicons were recovered from the two controls and 50% (15/30) of the samples screened. Fourteen were successfully typed, of which, 7.1% (1/14), 21.4% (3/14), 64.3% (9/14) and 7.1% (1/14) were enterovirus (EV) -A, EV-B, EV-C and a mixture of EV-B and C (EV-C99 and E25), respectively. The two controls were identified as EV-C99 and coxsackievirus (CV) -A1, both of which belong to the species Enterovirus C. In one sample, poliovirus serotype 2 was detected and found to have the VP1 ILE 143 variation and was therefore identified as a vaccine strain. The results of this study showed that significant proportion of enterovirus infections (including some with Sabin PV2) are being missed by the RD-L20B-cell-culture-based algorithm, thus highlighting the value of the RT-snPCR assay and its modifications. The circulation and preponderance of EV-C in Nigeria was also confirmed.