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We report the complete genome sequences of nine double recombinant vaccine-derived novel oral poliovirus type 2 genomes from acute flaccid paralysis (AFP) cases ( n = 3), AFP case contacts ( n = 4), and environmental surveillance sampling ( n = 2) in Nigeria.

After a long global battle with wild poliovirus, the virus has been defeated through researches and vaccination using the oral polio vaccine and inactivated polio vaccine as well as sensitization. The issue that is now of global concern is that of vaccine-derived poliovirus which emerged from the unstable oral polio vaccine. Ninety sewage water samples were collected from slums in Maiduguri using grab method, concentrated using two phase separation method and subjected to intratypic differentiation and vaccine-derived poliovirus screening. The result revealed the presence of Sabin 1in 17 samples (61.0%) and Sabin 3 in 22 samples (79.0%), all of which were positive after vaccine-derived poliovirus screening. The presence of strains of Sabin 1 and Sabin 3 in the sewage water samples collected is an indication of virus shedding in individuals which could be as a result of vaccination or contact with the faeces infected or vaccinated individuals., Competing Interests: Conflict Of Interest: Authors declared no conflict of interest.

Introduction: Although environmental and human behavioral factors in countries with Zika virus (ZIKV) outbreaks are also common in Nigeria, such an outbreak has not yet been reported probably due to misdiagnosis. The atypical symptoms of malaria and ZIKV infections at the initial phase could leverage their misdiagnosis. This study randomly recruited 496 malaria-suspected patients who visited selected health institutions in Adamawa, Bauchi, and Borno states for malaria tests. These patients' sera were analyzed for ZIKV antibodies using ELISA and plaque reduction neutralization tests (PRNT) at 90% endpoint. About 13.8% of Zika virus-neutralizing antibodies (nAb) did not cross-react with dengue, yellow fever, and West Nile viruses suggesting possible monotypic infections. However, 86% of the sera with ZIKV nAb also neutralized other related viruses at varied degrees: dengue viruses (60.7%), West Nile viruses (23.2%), yellow fever virus (7.1%) and 39.3% were co-infections with chikungunya viruses. Notably, the cross-reactions could also reflect co-infections as these viruses are also endemic in the country. The serum dilution that neutralized 90-100% ZIKV infectivity ranged from 1:8 to 1:128. Also, our findings suggest distinct protection against the ZIKV between different collection sites studied. As indicated by nAb, acute ZIKV infection was detected in 1.7% of IgM-positive patients while past infections occurred in 8.5% of IgM-negatives in the three states. In Borno State, 9.4% of IgG neutralized ZIKV denoting past infections while 13.5% were non-neutralizing IgM and IgG indicating other related virus infections. The age, gender, and occupation of the patients and ZIKV nAb were not significantly different. ZIKV nAb from samples collected within 1-7 days after the onset of symptoms was not significantly different from those of 7-10 days. A wider interval with the same techniques in this study may probably give better diagnostic outcomes. ZIKV nAb was significantly distinct among recipients and non-recipients of antibiotic/antimalaria treatments before seeking malaria tests. The inhibiting effect of these drugs on ZIKV infection progression may probably contribute to the absence of neurological disorders associated with the virus despite being endemic in the environment for several decades. Also, protection against ZIKV as marked by the nAb was different among the vaccinated and unvaccinated YF vaccine recipients. Thus, the YF vaccine may be a good alternative to the Zika vaccine in resource-constrained countries., Conclusion: The cryptic ZIKV infections underscore the need for differential diagnosis of malaria-suspected febrile patients for arboviruses, especially the Zika virus. The absence of systemic surveillance for the virus is worrisome because of its association with neurological disorders in newborns. Co-infections with other arboviruses may impact adversely on the management of these diseases individually., Competing Interests: The authors declare that the study was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2023 Baba et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

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.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.

Background: Management and control of the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus SARS-CoV-2 is critically dependent on quick and reliable identification of the virus in clinical specimens. Detection of viral RNA by a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a simple, reliable and cost-effective assay, deployable in resource-limited settings (RLS). Our objective was to evaluate the intrinsic and extrinsic performances of RT-LAMP in RLS., Methods: This is a multicenter prospective observational study of diagnostic accuracy, conducted from October 2020 to February 2021 in four African Countries: Cameroon, Ethiopia, Kenya and Nigeria; and in Italy. We enroled 1657 individuals who were either COVID-19 suspect cases, or asymptomatic and presented for screening. RNA extracted from pharyngeal swabs was tested in parallel by a colorimetric RT-LAMP and by a standard real time polymerase chain reaction (RT-PCR)., Findings: The sensitivity and specificity of index RT LAMP compared to standard RT-PCR on 1657 prospective specimens from infected individuals was determined. For a subset of 1292 specimens, which underwent exactly the same procedures in different countries, we obtained very high specificity (98%) and positive predictive value (PPV = 99%), while the sensitivity was 87%, with a negative predictive value NPV = 70%, Stratification of RT-PCR data showed superior sensitivity achieved with an RT-PCR cycle threshold (Ct) below 35 (97%), which decreased to 60% above 35., Interpretation: In this field trial, RT-LAMP appears to be a reliable assay, comparable to RT-PCR, particularly with medium-high viral loads (Ct < 35). Hence, RT-LAMP can be deployed in RLS for timely management and prevention of COVID-19, without compromising the quality of output., Competing Interests: The authors declare that this study was supported by the Bill & Melinda Gates Foundation [Grant Number INV-022,816]. Furthermore, New England Biolabs provided reagents free of charge. The authors have no additional interests to declare., (© 2021 The Authors.)

Poor systematic surveillance for Yellow Fever virus (YFV) is primarily due to lack of affordable diagnostic facilities in resource-constrained countries. This study aimed at providing evidence-based information on immunity against Yellow Fever with a view to assessing the possibility of the recent epidemics persisting in Nigeria. Six hundred patients with febrile illness seeking malaria test in selected hospitals were tested for YFV antibody using three serological assays: ELISA IgM, microneutralization test (MNT) and plaque reduction neutralization test (PRNT). The three assays commonly detected YFV antibody (Ab) in 1.7% patients, MNT: IgM in 8.3%, IgM: PRNT in 7.1%, and MNT: PRNT in 3.2%. Immunity against YF was significantly higher in Bauchi and Borno than Adamawa and children aged 0-9 years compared to 20-29 years. YFV neutralizing antibody (nAb) strongly correlated with the vaccination status of the patients. More unvaccinated patients had nAb compared with the vaccinated. Immunity against YF among treated patients with antibiotic and/or antimalaria before sample collection inversely correlated with the untreated. YVnAb among unvaccinated indicates natural infections. Acute YFV infections were mistaken for malaria and natural infections are ongoing. Individuals aged more than or equal to  20 years should be targeted during mass vaccination campaigns. With low population immunity, repetitive YF epidemics in Nigeria is not yet over. The current policy on Yellow Fever vaccination in Nigeria still leaves a large unimmunized population at the risk of epidemics. Sufficient mass vaccination in combination with National Programme on Immunization remains key to averting YF epidemics., (© 2021 Wiley Periodicals LLC.)

Objective: T-helper cells (Th)-1& -2 cytokines homeostasis control or predict clinical outcome of infected persons, especially those with HIV /AIDS. This case-control study evaluated the leucocytes differentials, TNF-alpha, interleukin (IL)-2 and -10 levels among HIV infected persons with serological evidence of leishmaniasis attending University of Abuja Teaching Hospital, Nigeria., Materials and Methods: Blood samples from 28 HIV infected persons who had Leishmania donovani rK39 and Immunoglobulin-G (IgG) positive (group 1), 30 age- & -sex matched HIV infected persons without Leishmania antibodies (group 2) and 30 apparently healthy persons without HIV and Leishmania antibodies (group 3). Full blood counts, TNF alpha, IL-2 and -10 levels were analyzed using automated hematology analyzer and ELISA, respectively. Structured questionnaires were used to collate biodata and clinical presentations of participants., Results: Ten (35.7%) participants in group 1 were on ART, 15 (50%) in group 2 were on ART, while group 3 were ART naïve. There were significantly higher values in basophil (4.4±2.5%) and eosinophil counts (12.9±3.8%) in HIV/leishmania coinfected persons (p<0.005). However, other white cells subpopulation was significantly lower in HIV/leishmania co-infected participants (p<0.05). There was significantly reduced CD4+ T cell counts ([119±26 versus 348±63 versus 605±116 cells/mm3]), TNF-alpha ([36.82±8.21 versus 64.67±12.54 versus 254.98±65.59 pg/mL]) and IL-2 levels ([142.14±20.91 versus 507.6±84.42 versus 486.62±167.87 pg/mL]) among HIV/Leishmania co-infected participants compared to group 2 and group 3 participants, respectively. However, higher IL-10 level (80.35±14.57 pg/mL) was found in HIV/Leishmania co-infected participants as opposed to the HIV monoinfected (62.2±10.43 pg/mL) and apparently healthy persons (23.97±4.88 pg/mL) (p<0.001)., Conclusion: Eosinophil, basophil counts and serum IL-10 level were high in HIV/Leishmania coinfected persons, demonstrating parasite-induced hypersensitivity and immunosuppression., Competing Interests: Conflict of Interest: Authors have no conflicts of interest to declare., (©Copyright 2020 by the Atatürk University School of Medicine - Available online at www.eurasianjmed.com.)

The burden of Arboviral infections is largely underestimated in Africa, particularly in North-Eastern Nigeria. A total of 200 serum samples were collected from patients exhibiting febrile illness who visited the State Specialist Hospital in Maiduguri for medical attention between March and April 2018. Sera were tested for Flavivirus RNA by a pan-flaviviral primer set using hemi-nested RT PCR. Twenty-six samples were positive for flaviviral RNA and sequence analysis indicated a high number of West Nile virus infections and one case of Zika virus. In-house recombinant NS1-based IgM ELISA indicated 47 % of WNV and 22 % of ZIKV infections. These data were also compared to commercially available assays for West Nile and Zika viruses. Finally, NS1 IgG ELISA was conducted for Dengue, Zika, West Nile and Usutu viruses. For serum samples detected by at least one flavivirus, 945% tested positive by NS1 IgG antibodies, while only 5.5 % of the patients were negative for all. To conclude, there is a high prevalence rate of arbovirus infections in the region, including Zika and Usutu viruses that were not previously detected. Interestingly, the analysis was conducted using in-house tools to allow the implementation of a sustainable surveillance protocol locally., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Objective: Coronavirus disease 2019 (COVID-19) has caused an unprecedented global health emergency. The COVID-19 pandemic has claimed over 350,000 human lives within five months of its emergence, especially in the USA and the European continent. This study analysed the implications of the genetic diversity and mutations in SARS-CoV-2 on its virulence diversity and investigated how these factors could affect the successful development and application of antiviral chemotherapy and serodiagnostic test kits, and vaccination., Methods: All the suitable and eligible full text articles published between 31st December 2019 and 31st May 2020 were filtered and extracted from "PubMed", "Scopus", "Web of Science", and "Hinari" and were critically reviewed. We used the Medical Subject Headings (MeSH) terms "COVID-19, "Mutation", "Genetic diversity", "SARS-CoV-2", "Virulence", "Pathogenicity", "Evolution" and "SARS-CoV-2 transmission" for this search., Results: Our search showed that SARS-CoV-2 has persistently undergone significant mutations in various parts of its non-structural proteins (NSPs) especially NSP2 and NSP3, S protein, and RNA-dependent RNA polymerase (RdRp). In particular, the S protein was found to be the key determinant of evolution, transmission, and virulence of SARS-CoV-2, and could be a potential target for vaccine development. Additionally, RdRp could be a major target in the development of antivirals for the treatment of COVID-19., Conclusion: Given the critical importance of mutations in the pathogenicity of SARS-CoV-2 and in the development of sero-diagnostics, antivirals, and vaccines, this study recommends continuous molecular surveillance of SARS-CoV-2. This approach would potentially prompt identification of new mutants and their impact on ongoing biomedical interventions and COVID-19 control measures., (© 2020 The Authors.)

Chikungunya (CHIK) is a re-emerging and myo-arthritogenic arboviral infection that has affected significant global population. However, CHIK is a neglected disease in Nigeria. This study aimed to estimate the pooled prevalence pattern of CHIK virus infection in Nigeria. A systematic review of eligible articles was conducted from "PubMed", "Scopus", "Google Scholar" and "Web of Science", between January 1980 to February 2020. Peer-reviewed articles describing CHIKV infection in cross-sectional studies were systematically reviewed. Random-effect model was used to pool the prevalence of CHIKV infection and associated sociodemographic data reported from eligible studies. In total, there were 10 published articles on CHIKV infection. Of these, 7 were cross-sectional studies, which comprised of 1347 pooled participants. The pooled anti-CHIKV IgM and IgG seroprevalence were 26.7% (95% CI: 23.2 - 30.4) and 29.3% (95% CI: 26.2 -32.6), respectively.  Of the pooled studies, there were 3.8% (95% CI: 2.0-6.4) CHIKV RNA positive cases and 46.1% prevalence of CHIKV neutralizing antibodies. Of the 6 geopolitical zones in Nigeria, Northeast had the highest serological evidence of CHIKV infection. There was a significance association between the prevalence of anti-CHIKV and geopolitical zones of Nigeria ( χ² = 70.04; p˂0.0001). Sex (p ˂0.0001; OR= 1.87 [1.47 - 2.38]) and level of education (p ˂0.0001; OR= 2.74 [1.89 - 3.95]) were significant risk factors for pooled anti-CHIKV IgM seropositivity. However, no significant association was found with other sociodemographic variables (p ˃0.05). Although there was paucity of data on CHIKV research in Nigeria, this meta-analysis revealed a high prevalence of CHIKV infection in the country.

Group A rotaviruses (RVA) are the leading cause of acute gastroenteritis (AGE) in children worldwide and cause up to 455,000 deaths annually, mostly in developing countries. During 2013, 66 RVAs from children with AGE admitted to four Nigerian hospitals were investigated. The G3P[6], G1P[8] and G2P[4] genotypes predominated. The VP7 and/or VP4 genes of 18 G3P[6]/[8]/[4], six G2P[4], three G12P[8]/[4], and two G1P[8] RVA strains were sequenced. The G3P[6] strains belonged to lineage G3-III and were different from G3 strains widespread in Asia. Phylogenetic analysis revealed substantial sequence conservation, suggesting continuing evolution and genomic reassortment but no zoonotic RVA transmission from animals.

Deep sequencing of untreated sewage provides an opportunity to monitor enteric infections in large populations and for high-throughput viral discovery. A metagenomics analysis of purified viral particles in untreated sewage from the United States (San Francisco, CA), Nigeria (Maiduguri), Thailand (Bangkok), and Nepal (Kathmandu) revealed sequences related to 29 eukaryotic viral families infecting vertebrates, invertebrates, and plants (BLASTx E score, <10(-4)), including known pathogens (>90% protein identities) in numerous viral families infecting humans (Adenoviridae, Astroviridae, Caliciviridae, Hepeviridae, Parvoviridae, Picornaviridae, Picobirnaviridae, and Reoviridae), plants (Alphaflexiviridae, Betaflexiviridae, Partitiviridae, Sobemovirus, Secoviridae, Tombusviridae, Tymoviridae, Virgaviridae), and insects (Dicistroviridae, Nodaviridae, and Parvoviridae). The full and partial genomes of a novel kobuvirus, salivirus, and sapovirus are described. A novel astrovirus (casa astrovirus) basal to those infecting mammals and birds, potentially representing a third astrovirus genus, was partially characterized. Potential new genera and families of viruses distantly related to members of the single-stranded RNA picorna-like virus superfamily were genetically characterized and named Picalivirus, Secalivirus, Hepelivirus, Nedicistrovirus, Cadicistrovirus, and Niflavirus. Phylogenetic analysis placed these highly divergent genomes near the root of the picorna-like virus superfamily, with possible vertebrate, plant, or arthropod hosts inferred from nucleotide composition analysis. Circular DNA genomes distantly related to the plant-infecting Geminiviridae family were named Baminivirus, Nimivirus, and Niminivirus. These results highlight the utility of analyzing sewage to monitor shedding of viral pathogens and the high viral diversity found in this common pollutant and provide genetic information to facilitate future studies of these newly characterized viruses.

Despite significant success of the Global Polio Eradication Initiative (GPEI) in Nigeria, Afghanistan, India, Pakistan, wild poliovirus still occurs due to persistently high proportions of under and unimmunized children. The study aimed at determining the type of poliovirus often excreted into the environment. Four hundred nine fecal samples collected from apparently healthy school children aged 5-16 years in Borno and Adamawa States, northeastern Nigeria, were tested for poliovirus by tissue culture technique. The isolates were characterized further by intratypic differentiation testing and genetic sequencing. Three wild poliovirus type, 11 Sabin type, combination of Sabin-types 1 + 2 and 2 + 3 poliovirus, and 22 non-polio enteroviruses were obtained. The continued excretion of wild-type poliovirus among children above 5 years old vaccinated with oral polio vaccine contributes to the persistent circulation of these viruses in the environment and may limit the population immunity. However, the excreted Sabin poliovirus is capable of immunizing the unvaccinated children and promotes herd immunity. Similarly, the excretion of combination of two polio serotypes indicates the child susceptibility to the missing serotype (s) and therefore indicates an immunity gap. The common unhygienic practices in the environment could aid the spread of these viruses through oral-fecal route. Asymptomatic transmission of wild poliovirus among older oral polio vaccine-vaccinated children poses a serious threat to polio eradication program in Nigeria and therefore, environmental and serological surveillance with larger sample size are important for monitoring poliovirus circulation in Nigeria., (Copyright © 2011 Wiley Periodicals, Inc.)

A new species of parvovirus, tentatively named human bocavirus 4 (HBoV4), was genetically characterized. Among 641 feces samples obtained from children and adults, the most commonly detected bocavirus species were, in descending order, HBoV2, HBoV3, HBoV4, and HBoV1, with an HBoV2 prevalence of 21% and 26% in Nigerian and Tunisian children, respectively. HBoV3 or HBoV4 species were found in 12 of 192 patients with non-polio acute flaccid paralysis in Tunisia and Nigeria and 0 of 96 healthy Tunisian contacts (P = .01). Evidence of extensive recombination at the NP1 and VP1 gene boundary between and within bocavirus species was found. The high degree of genetic diversity seen among the human bocaviruses found in feces specimens, relative to the highly homogeneous HBoV1, suggest that this worldwide-distributed respiratory pathogen may have recently evolved from an enteric bocavirus after acquiring an expanded tropism favoring the respiratory tract. Elucidating the possible role of the newly identified enteric bocaviruses in human diseases, including acute flaccid paralysis and diarrhea, will require further epidemiological studies.

A novel picornavirus genome was sequenced, showing 42.6%, 35.2%, and 44.6% of deduced amino acid identities corresponding to the P1, P2, and P3 regions, respectively, of the Aichi virus. Divergent strains of this new virus, which we named salivirus, were detected in 18 stool samples from Nigeria, Tunisia, Nepal, and the United States. A statistical association was seen between virus shedding and unexplained cases of gastroenteritis in Nepal (P = 0.0056). Viruses with approximately 90% nucleotide similarity, named klassevirus, were also recently reported in three cases of unexplained diarrhea from the United States and Australia and in sewage from Spain, reflecting a global distribution and supporting a pathogenic role for this new group of picornaviruses.