Serological detection of human T-cell lymphotropic virus types I and II among pregnant women in Ilorin, Nigeria.

Human T-cell lymphotropic virus types I/II (HTLV-I/II) is endemic in some parts of the world including Nigeria. Reported prevalence rates in Nigeria have largely focused on blood donors. This study aims at determining the prevalence of HTLV infection among pregnant women in Ilorin North-central Nigeria. Serum samples from 276 pregnant women who were antenatal clinic attendees at General and Civil Service Hospitals in Ilorin were tested for the presence of HTLV-I/II antibodies using Enzyme Linked Immunosorbent Assay test kits from Diagnostic Automation INC., USA. Out of the 276 women tested, 3 tested positive giving a prevalence rate of 1.1%. The result was analyzed on the basis of age, marital status, nature of family, educational status, occupation, religion, parity, and gestational stage of the women. There was no statistical association of HTLV positivity with any of the variables. Although relatively lower than prevalence rate recorded among similar study groups in other parts of the country, the 1.1% prevalence in this study underscores the need for proper education and creation of awareness among antenatal clinic attendees, so as to reduce viral transmission and incidence of HTLV-related diseases.

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 20th, 2020 and March 20th, 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.

Detection of novel paramyxoviruses in Chaerephon bat species in Nigeria and phylogenetics of paramyxoviruses co-evolution with bats in Africa.

Bat paramyxoviruses (PmV) are a diverse group of viruses and include zoonotic viruses such as henipaviruses. Members of this group in other continents have been associated with severe respiratory and neurological infections in animals and humans. Furthermore, despite the richness of diverse bat species that can transmit this virus in African countries like Nigeria, there is very scanty information as to the presence and co-evolution of paramyxoviruses in bats. There is a need for continuous surveillance of zoonotic viruses and their biological reservoirs as this will help in the prevention and management of pathogens' spillovers. This study detected novel paramyxoviruses in Chaerephon nigeriae bat species found in Badagry, Lagos. Phylogenetic analyses of paramyxovirus sequences' co-evolution with frugivorous and insectivorous bats circulating in African countries were also performed using sequences of African origin available in the Database of Bat-Associated Viruses (DBatVir: http://www.mgc.ac.cn/DBatVir/). Oral swabs (n = 18) and blood samples (n = 32) were collected from C. nigeriae bats in Badagry, Lagos. The L gene of bat paramyxovirus was detected in all oral swabs using PCR techniques. Six of the amplicons were successfully sequenced. Estimated phylogenies placed the sequences in close relationship with those isolated from insectivorous bats. Phylogenetic analyses of previously sequenced isolates in the African region showed the likelihood of different co-evolution mechanisms of paramyxoviruses with frugivorous bats compared with insectivorous bats. This may be due to codon usage bias of the L gene. Spatial distribution of paramyxoviruses in African countries showed limited ongoing surveillance of this virus in the continent, especially in southern and northern countries. Extensive surveillance of paramyxoviruses with possible zoonotic potentials among bat species in the continent is recommended. This will provide further insights into co-evolution as well as prevent possible spillover into the human population.

Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences.

BACKGROUND: The ongoing SARS-CoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing a severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months, between 14th February to 24th April 2020, using whole genome sequences. METHODS: We performed recombination analysis against closely related CoV strains, Bayesian time scaled phylogeny, and investigation of spike protein amino acid mutations. RESULTS: Recombination signals were observed between the Afr-SARS-CoV-2 sequences and reference sequences within the RdRPs and S genes. The evolutionary rate of the Afr-SARS-CoV-2 was 4.133 × 10-4 Highest Posterior Density (HPD 4.132 × 10-4 to 4.134 × 10-4) substitutions/site/year. The time to most recent common ancestor (TMRCA) of the African strains was December 7th 2019, (95% HPD November 12th 2019-December 29th 2019). The Afr-SARCoV-2 sequences diversified into two lineages A and B, with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility (MCC) tree and PANGOLIN software. There was a high prevalence of the D614G spike protein amino acid mutation 59/69 (82.61%) among the African strains. CONCLUSION: This study has revealed a rapidly diversifying viral population with the G614G spike protein variant dominatinge advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARS-CoV-2 in Africa.

Detection of Dengue viruses among febrile patients in Lagos, Nigeria and phylogenetics of circulating Dengue serotypes in Africa.

Dengue fever, a mosquito borne viral disease, is caused by Dengue virus. This virus and its vector is endemic in most tropical countries including Nigeria. Dengue presents with febrile symptoms and is a major cause of morbidity and mortality in affected countries. The infection presently has no licensed drugs and vaccine is only available for previously exposed individuals. Despite the endemicity of Dengue in Nigeria, very few studies have identified circulating Dengue genotypes in the country. There is also sparse information on the occurrence, distribution and temporal patterns of circulating dengue virus serotypes as well as genotypes in Africa. This situation creates barriers to effective control of the infection in the continent. This study identified Dengue serotypes and genotypes among febrile patients in two health centers in Lagos, Nigeria. Phylogenetic analysis of Dengue sequences previously collected from African countries and submitted to GenBank database from 1944 till date was also performed. One hundred and thirty febrile persons were recruited for the study between April and August 2018. Eleven (8.5%) persons were Dengue virus positive. Dengue virus serotypes 1 (genotype I) and 3 (genotype I) were identified as actively circulating in Lagos, Nigeria. DENV 1 genotype V, DENV 2 cosmopolitan genotype and DENV 3 genotype III has over the years been the predominant circulating Dengue strains in Africa. Relative genotypic stability of circulating Dengue serotypes in Africa occurred over the past five decades. This may be due to limited investigations on circulating Dengue serotypes among asymptomatic individuals in the region as most studies focused on disease outbreaks and imported cases. There is the need to describe circulating Dengue genotypes in northern Africa, southern Africa as well as among asymptomatic individuals in other parts of Africa as this will provide further information on the diversity of Dengue genotypes circulating in the region.

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.

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.