Seromolecular survey and risk factor analysis of Crimean-Congo haemorrhagic fever orthonairovirus in occupationally exposed herdsmen and unexposed febrile patients in Kwara State, Nigeria.

Crimean-Congo haemorrhagic fever virus (CCHFV) is a globally significant tick-borne zoonotic pathogen that causes fatal haemorrhagic disease in humans. Despite constituting an ongoing public health threat, limited research exists on the presence of CCHFV among herdsmen, an occupationally exposed population that has prolonged contact with ruminants and ticks. This cross-sectional study, conducted between October 2018 and February 2020 in Kwara State, Nigeria, was aimed at assessing CCHFV seroprevalence among herdsmen and non-herdsmen febrile patients, and identifying the associated risk factors. Blood samples from herdsmen (n = 91) and febrile patients in hospitals (n = 646) were analyzed for anti-CCHFV IgG antibodies and CCHFV S-segment RNA using ELISA and RT-PCR, respectively. Results revealed a remarkably high CCHFV seroprevalence of 92.3% (84/91) among herdsmen compared to 7.1% (46/646) in febrile patients. Occupational risk factors like animal and tick contact, tick bites, and hand crushing of ticks significantly contributed to higher seroprevalence in the herdsmen (p<0.0001). Herdsmen were 156.5 times more likely (p<0.0001) to be exposed to CCHFV than febrile patients. Notably, the odds of exposure were significantly higher (OR = 191.3; p<0.0001) in herdsmen with a history of tick bites. Although CCHFV genome was not detectable in the tested sera, our findings reveal that the virus is endemic among herdsmen in Kwara State, Nigeria. CCHFV should be considered as a probable cause of febrile illness among humans in the study area. Given the nomadic lifestyle of herdsmen, further investigations into CCHF epidemiology in this neglected population are crucial. This study enhances our understanding of CCHFV dynamics and emphasizes the need for targeted interventions in at-risk communities.

Prevalence and risk factors for high-risk human papillomavirus infection among women from three southern geopolitical zones of Nigeria.

Introduction: Human Papillomavirus (HPV) infection is a risk factor for cervical cancer, the fourth most common cancer among women globally. Its burden is the highest in sub-Saharan Africa, with over 90% mortality. Interventions may fail without evidence-based data on stratified prevalence and risk factors among most at-risk women across Nigeria. Methods: A cross-sectional comparative study, with participants recruited from the Nigerian Institute of Medical Research's Clinics, NGO outreaches, a cancer screening centre and a university teaching hospital. Questionnaires were self-administered. Trained medics performed sampling at healthcare facilities, and self-sampling was used at outreaches. Results: Nine hundred eighty-five study participants were recruited. About 37% and 27% of the women knew about HPV and its vaccines, respectively, but only 6% confirmed vaccination with HPV vaccines. HPV prevalence was highest among women with unknown marital status (35.9%), single women (33.8%), widowed/divorced/separated women (30.3%), and married/cohabiting women (19.6%). HPV infection was significantly higher among women who take alcohol (odds=1.7 [95% CI: 1.2-2.4]) and women who smoke (odds=2.6 [95% CI: 1.4 - 4.6]. HPV strains detected included HPV16 (1.3%), HPV18 (1.5%), Low Risk (0.2%) and Other High-Risk groups (19.7%). Conclusion: The inverse relationship between prevalence and education suggests interventions improving awareness and prevention would be impactful. Such interventions could also target HIV-positive women, women presenting with sexually-transmitted infections, who smoke and frequently drink alcohol.

Seromolecular surveillance of rabbit haemorrhagic disease virus in Nigeria.

Following the first 2020 rabbit haemorrhagic disease virus (RHDV) outbreak in Nigeria which caused massive mortalities in several rabbitries, there was a need to know the spread and strains circulating in the affected states. Over 100 rabbitries still existing post-RHDV outbreak in Ogun and Kwara States were investigated. A commercial enzyme-linked immunosorbent assay kit was used to screen for RHDV immunoglobulin G in 192 rabbit sera, while RHDV VP60 gene was amplified in RNA extracted from these sera and tissues (liver and/or spleen harvested from 37 carcasses necrotized) by reverse transcription-polymerase chain reaction (RT-PCR). Sequences obtained from the amplicons were subjected to phylogenetic analysis. The results revealed a seroprevalence of 82.3% (158/192). RHDV VP60 gene was detected in 15/17 (88.2%) and 2/20 (10.0%) carcasses from Ogun and Kwara States, respectively, while none of the sera was positive. Sequences of the two positive amplicons selected (one from each states) shared 98.95% nucleotide identity and belonged to RHDV 2/GI.2 strain. Also, nBLAST of these sequences revealed 98.43-99.55% homology with the prototype Nigerian RHDV strain RHDV/NGR/ILN/001 (MT996357.1). Furthermore, these strains clustered with this prototype and a German RHDV strain (LR899166.1). Pathologic lesions affecting the respiratory, cardiovascular, renal, lymphatic, and digestive systems were observed in necropsied carcasses. This study indicated that RHDV 2/GI.2 strain was the cause of 2020 RHD outbreak in Nigeria. Thus, while continuous public sensitization about RHD especially among rabbit farmers in Nigeria is important, efforts aimed at design and implementation of RHD vaccination policy, preferably using indigenous seed, should be expedited.

Molecular surveillance of arboviruses in Nigeria.

Arboviral infections are fast becoming a global public health concern as a result of its high fatality rate and sporadic spread. From the outbreak of Zika virus in the Americas, the endemicity of Yellow fever in West Africa and South America, outbreaks of West Nile virus in South Africa to the year-round and national risk of Dengue fever in Mainland China and India. The war against emerging and re-emerging viral infection could probably lead to the next pandemic. To be above the pending possible arboviral pandemic, consistent surveillance of these pathogens is necessary in every society. This study was aimed at conducting a surveillance for Yellow fever virus, Zika virus, Chikungunya virus, Dengue virus and Rift Valley fever virus in four states in Nigeria using molecular techniques. A cross-sectional study involving 1600 blood samples collected from febrile patients in Lagos, Kwara, Ondo and Delta States between 2018 and 2021 was conducted using Real time polymerase chain reaction for detection of the pathogens. Extraction and purification of viral RNA were done using Qiagen Viral RNA Mini Kit. Samples were analyzed using One Step PrimeScript III RT-PCR mix (Takara Bio) alongside optimized primers and probes designed in-house. Positive samples were sequenced on MinION platform (Nanopore technologies). Bioinformatic and phylogenetic analysis were performed with DNASTAR Lasergene 17.3. All the RNA extracted from samples collected from the four states were negative for ZIKV RNA, RVFV RNA, CHIKV RNA and DENV RNA. However, twelve of the samples (2%) tested positive for YFV RNA. Three full genomes of sizes 10,751 bp, 10,500 bp and 10,715 bp were generated and deposited in GenBank with accession numbers: ON323052, ON323053 and ON323054 respectively. Phylogenetic analysis shows clustering within lineage 3 of West African genotype. This result shows an active spread of Yellow fever in Delta State, Nigeria. However, there is no emergence of a new genotype There is a need for an intense surveillance of Yellow fever virus in Nigeria to avert a major outbreak.

Self-collected versus medic-collected sampling for human papillomavirus testing among women in Lagos, Nigeria: a comparative study.

OBJECTIVE: To evaluate the feasibility and performance of self-collected vaginal swab samples for HPV screening among women in Lagos, Nigeria. METHODS: A cross-sectional study was implemented from March to August 2020 among sexually active women. Study participants provided same-day paired vaginal swab samples. Medic-sampling and poster-directed self-sampling methods were used to collect the two samples per participant. A real-time PCR assay detected HPV 16, HPV 18, other-high-risk (OHR) HPV, and the human ß-globin gene. The self-collected samples' sensitivity, specificity, and accuracy were determined against the medic-collected samples using the MedCalc Online Diagnostic Calculator. RESULTS: Of the 213 women aged 16 ~ 63-year-old recruited, 187 (88%) participants had concordant results, while 26 (12%) participants had discordant results. Among the 187 concordant results, 35 (19%) were HPV positive, 150 (80%) participants were HPV negative, and two (1%) were invalid. 18 (69%) out of the 26 discordant samples were invalid. The self-collected sample was invalid for 14 (54%) participants. Two (8%) medic-collected samples were invalid. Compared to the medic-collected sample, the self-collected sample was 89.80% (95% CI: 77.77 ~ 96.60%) sensitive and 98.21% (95% CI: 94.87 ~ 99.63%) specific, with an accuracy of 96.31% (95% CI: 92.87 ~ 98.40%). The mean age for HPV positive and negative participants were 39 and 40, respectively, with an ANOVA p-value of 0.3932. The stratification of HPV infection by the age group was not statistically significant (P > 0.05). CONCLUSIONS: With high accuracy of 96%, self-collected sampling is adequate when tested with real-time PCR and may increase the uptake of HPV testing. Though more self-collected samples were invalid than medic-collected samples, most likely due to poor collection, they could be identified for repeat testing. Future implementation can avoid this error with improved guidance and awareness.

Low level SARS-CoV-2 RNA detected in plasma samples from a cohort of Nigerians: Implications for blood transfusion.

The present global pandemic triggered by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has lingered for over a year in its devastating effects. Diagnosis of coronavirus disease 2019 (COVID-19) is currently established with a polymerase chain reaction (PCR) test by means of oropharyngeal-, nasopharyngeal-, anal-swabs, sputum and blood plasma. However, oral and nasal swabs are more commonly used. This study, therefore, assessed sensitivity and specificity of plasma as a diagnostic in comparison with a combination of oral and nasal swab samples, and the implications for blood transfusion. Oropharyngeal (OP) and nasopharyngeal (NP) swab samples were obtained from 125 individuals suspected to have COVID-19 and stored in viral transport medium (VTM) tubes. Ten millilitres of blood samples in EDTA were also obtained by venepuncture and spun to obtain plasma. Viral RNA was obtained from both swabs and plasma by manual extraction with Qiagen QIAamp viral RNA Mini Kit. Detection was done using a real time fluorescent RT-qPCR BGI kit, on a QuantStudio 3 real-time PCR instrument. Average age of study participants was 41 years, with 74 (59.2%) being male. Out of the 125 individuals tested for COVID-19, 75 (60%) were positive by OP/NP swab. However, only 6 (4.8%) had a positive plasma result for COVID-19 with median Ct value of 32.4. Sensitivity and specificity of RT-PCR SARS-CoV-2 test using plasma was 8% and 100% respectively. There was no false positive recorded, but 69 (55.2%) false negatives were obtained by plasma. SARS-CoV-2 viral RNA was detected, albeit low (4.8%) in plasma. Plasma is likely not a suitable biological sample to diagnose acute SARS-CoV-2 infection. The implication of transfusing blood in this era of COVID-19 needs further investigations.

Immunological screening of Lassa Virus among Health workers and Contacts of patients of Lassa fever in Ondo State.

BACKGROUND: The increasing trends of morbidity and mortality of Lassa fever is becoming more alarming in Nigeria. Information about immune response to the virus is limited. At exposure, the level of immunity plays a vital role in the vulnerability of individuals infected. OBJECTIVE: Investigating the immune status of health workers, infected cases and contacts of infected cases of Lassa fever in Ondo State. STUDY DESIGN: Blood samples were collected from 233 individuals comprising 102 health workers, 22 infected cases and 109 contacts of infected cases from Owo and Ose Local Government Areas and transported in triple level packaging. Plasma samples were analyzed for IgG and IgM markers using ReLASV® Pan-Lassa NP IgG/IgM ELISA Kit (Zalgen Labs, LLC, USA) while RNAs extracted from IgM positive samples were analyzed for LASV RNA according to manufacturers' instructions. RESULT: Among the health workers, 20/102 (19.6%) and 2/102 (2.0%) were IgG and IgM positive respectively. While 16/22 (72.7%) and 14/22 (63.6%) were IgG and IgM positive respectively among the infected cases. Of the contacts of infected cases screened, 64/109 (58.7%) were IgG positive while 4/109 (3.7%) were positive for IgM. There was no detectable LASV RNA in the samples analyzed. CONCLUSION: These findings suggest that majority of the health workers are naïve to the virus and hence may be prone to the viral infection. It could also be suggestive that a good personal protective procedure is been practiced by the health workers, hence the low exposure. However, most of the contacts of infected cases show exposure to the virus.

Full length genomic sanger sequencing and phylogenetic analysis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Nigeria.

In an outbreak, effective detection of the aetiological agent(s) involved using molecular techniques is key to efficient diagnosis, early prevention and management of the spread. However, sequencing is necessary for mutation monitoring and tracking of clusters of transmission, development of diagnostics and for vaccines and drug development. Many sequencing methods are fast evolving to reduce test turn-around-time and to increase through-put compared to Sanger sequencing method; however, Sanger sequencing remains the gold standard for clinical research sequencing with its 99.99% accuracy This study sought to generate sequence data of SARS-CoV-2 using Sanger sequencing method and to characterize them for possible site(s) of mutations. About 30 pairs of primers were designed, synthesized, and optimized using endpoint PCR to generate amplicons for the full length of the virus. Cycle sequencing using BigDye Terminator v.3.1 and capillary gel electrophoresis on ABI 3130xl genetic analyser were performed according to the manufacturers' instructions. The sequence data generated were assembled and analysed for variations using DNASTAR Lasergene 17 SeqMan Ultra. Total length of 29,760bp of SARS-CoV-2 was assembled from the sample analysed and deposited in GenBank with accession number: MT576584. Blast result of the sequence assembly shows a 99.97% identity with the reference sequence. Variations were noticed at positions: nt201, nt2997, nt14368, nt16535, nt20334, and nt28841-28843, which caused amino acid alterations at the S (aa614) and N (aa203-204) regions. The mutations observed at S and N-gene in this study may be indicative of a gradual changes in the genetic coding of the virus hence, the need for active surveillance of the viral genome.

Monitoring of Lassa virus infection in suspected and confirmed cases in Ondo State, Nigeria.

INTRODUCTION: Lassa virus (LASV), the causative agent of Lassa fever (LF), an endemic acute viral haemorrhagic illness in Nigeria, is transmitted by direct contact with the rodent, contaminated food or household items. Person-to-person transmission also occurs and sexual transmission has been reported. Thus, this study investigated the presence of LASV in body fluids of suspected and confirmed cases. METHODS: this was a cross-sectional study between March 2018 and April 2019 involving 112 consenting suspected and post ribavirin confirmed cases attending the Lassa fever treatment center in Ondo State. Whole blood was collected from 57 suspected and 29 confirmed cases. Other samples from confirmed cases were 5 each of High Vaginal Swab (HVS) and seminal fluid; 12 breast milk and 4 urine. All samples were analyzed using reverse transcription-PCR (RT-PCR) targeting the S-gene of LASV. RESULTS: analysis of whole blood by RT-PCR showed that 1/57 (1.8%) suspected and 1/29 (3.4%) confirmed post ribavirin treated cases were positive. While LASV was detected in 2/5 (40%) post ribavirin treated seminal fluids and 1/11 (8.3%) breast milk. However, LASV was not detected in any of the HVS and urine samples. CONCLUSION: the detection of LASV in seminal fluid and breast milk of discharged post ribavirin treated cases suggests its persistence in these fluids of recovering Nigerians. The role of postnatal and sexual transmissions in the perennial outbreak of LF needs to be further evaluated.