Medical Microbiology & Parasitology
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Item A randomized, open-label trial of combined nitazoxanide and atazanavir/ritonavir for mild to moderate COVID-19(Frontiers Media, 2022-09) Fowotade, A.; Bamidele, F.; Egbetola, B.; Fagbamigbe, A. F.; Adeagbo, B. A.; Adefuye, B. O.; Olagunoye, A.; Ojo, T. O.; Adebiyi, A. O.; Olagunju, O. I.; Ladipo, O. T.; Akinloye, A.; Onayade, A.; Bolaji, O. O.; Rannard, S.; Happi, C.; Owen, A.; Olagunju, A.Background: The nitazoxanide plus atazanavir/ritonavir for COVID-19 (NACOVID) trial investigated the efficacy and safety of repurposed nitazoxanide combined with atazanavir/ritonavir for COVID-19. Methods: This is a pilot, randomized, open-label multicenter trial conducted in Nigeria. Mild to moderate COVID-19 patients were randomly assigned to receive standard of care (SoC) or SoC plus a 14-day course of nitazoxanide (1,000 mg b.i.d.) and atazanavir/ritonavir (300/100 mg od) and followed through day 28. Study endpoints included time to clinical improvement, SARS-CoV-2 viral load change, and time to complete symptom resolution. Safety and pharmacokinetics were also evaluated (ClinicalTrials.gov ID: NCT04459286). Results: There was no difference in time to clinical improvement between the SoC (n = 26) and SoC plus intervention arms (n = 31; Cox proportional hazards regression analysis adjusted hazard ratio, aHR = 0.898, 95% CI: 0.492–1.638, p = 0.725). No difference was observed in the pattern of saliva SARS-CoV- 2 viral load changes from days 2–28 in the 35% of patients with detectable virus at baseline (20/57) (aHR = 0.948, 95% CI: 0.341–2.636, p = 0.919). There was no significant difference in time to complete symptom resolution (aHR = 0.535, 95% CI: 0.251–1.140, p = 0.105). Atazanavir/ritonavir increased tizoxanide plasma exposure by 68% and median trough plasma concentration was 1,546 ng/ml (95% CI: 797–2,557), above its putative EC90 in 54% of patients. Tizoxanide was undetectable in saliva. Conclusion: Nitazoxanide co-administered with atazanavir/ritonavir was safe but not better than standard of care in treating COVID-19. These findings should be interpreted in the context of incomplete enrollment (64%) and the limited number of patients with detectable SARS-CoV-2 in saliva at baseline in this trial.Item Seroprevalence of anti-SARS-CoV-2 specific antibodies in vaccinated and vaccine naïve adult Nigerians(Plos One, 2023-01) Onifade, A. A.; Fowotade, A.; Rahamon, S. K.; Edem, V. F.; Yaqub, S. A.; Akande, O. K.; Arinola, O. G.Background Reports on the evaluation of immune responses to different COVID-19 vaccines are limited. Similarly, effects of age and gender have not been well explored as variables that could impact on the vaccine-induced antibody response. Therefore, seroprevalence of anti-SARS-CoV-2 specific antibodies in vaccinated and vaccine naïve adult Nigerians was determined in this study. Methodology A total of 141 adults were enrolled into this study. Presence or absence of SARS-CoV-2 infection was confirmed by real-time reverse-transcriptase polymerase-chain reaction (RT-PCR) assay on nasopharyngeal and oropharyngeal swab specimens. Anti-SARS-CoV-2 Specific IgG and IgM antibodies were qualitatively detected using a Rapid Diagnostic Test kit. Results Pre-vaccination, 77% of the study participants had never had PCR-confirmed COVID-19 test yet 66.7% of them were seropositive for SARS-CoV-2 antibodies. Of 111 COVID-19 vaccinated participants, 69.2% and 73.8% of them had SARS-CoV-2 specific IgG post-first and second doses of COVID-19 vaccine respectively. However, 23.1% and 21.4% of the participants who have had first and second doses respectively ha no detectable anti- SARS-CoV-2 antibodies. The proportion of participants with SARS-CoV-2 specific IgG was insignificantly higher in those between the ages of 18–40 years and 41–59 years compared with individuals aged �60 years. No significant association was observed between gender and seropositivity for SARS-CoV-2 antibodies. Conclusion There is high SARS-CoV-2 antibody seroprevalence among Nigerian adults who never had PCR-confirmed COVID-19. Also, there is the need for anti-SARS-CoV-2 antibodies screening post vaccination as this could be essential in achieving herd immunity. Age and gender do not seem to have significant association with seropositivity.Item A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS CoV-2 in seven Sub-Saharan African countries: Lessons from the field(Elsevier B.V., 2023) Ceruti, A.; Dia, N.; Bakarey, A. S.; Ssekitoleko, J.; Andriamandimby, S. F.; Malwengo-Kasongo, P.; Ahmed, R. H. A.; Kobialka, R. M.; Heraud, J. M.; Diagne, M. M.; Fowotade, A.Background: The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings. Objectives: To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries. Study design: In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 min. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied. Results: Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay). Conclusion: Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.Item Comparative analysis of Cervical Human Papillomavirus DNA testing and cytological findings among women presenting for “Pap” smear in a Tertiary Health Centre in Northern Nigeria(SCIENCE DOMAIN International, 2016) Manga, M. M.; Fowotade, A.; Abdullahi, Y. M.; El-Nafaty, A. U.; Adamu, S.; Bojude, A. D.; Pindiga, H. U.; Bakare, R. A.; Osoba, A. O.Aim: This study was conducted to compare different cytological findings with cervical HPV infection among women presenting for cervical cancer screening in Gombe north-eastern Nigeria. Study Design: It is a hospital based cross-sectional study. Place and Duration of Study: Departments of Obstetrics/Gynaecology and Histopathology Federal Teaching Hospital Gombe (FTHG) Nigeria, between August 2013 and May 2014. Methodology: Two hundred and nine (209) women were subjected to liquid-based cervical cytology and HPV DNA testing. Results: Of the 209 participants, cytological findings were normal in 126 (61.6%) women while 80 (39.0%) had abnormal features. Three (1.4%) respondents had unsatisfactory smears. The observed abnormal cytological features include HPV changes 30 (14.4%), HPV changes with inflammation 2 (1.0%), inflammatory changes alone 36 (17.3%), Low Squamous Intraepithelial Lesion; LSIL 3 (1.4%), High Squamous Intraepithelial Lesion; HSIL 5 (2.4%) and malignant changes 3 (1.4%). Positive HPV DNA testing was detected among 100 (48.1%) of the participants. Almost half 60 (47.6%) of the women with normal cytology were positive for HPV. Among women with cytologically detected HPV changes, only 16 (50%) were also HPV DNA positive. The sensitivity and specificity of cervical cytology in detecting HPV infection was 16.2% and 85.0% respectively. Conclusion: This study reports a very low sensitivity but relatively high specificity of cytology in detecting cervical HPV infection. It further justifies the need for introduction of HPV DNA testing to improve efficiency and maximise the sensitivity of cytology based cervical cancer screening for women above 30 years.Item Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria(Nature Portfolio, 2023-02) Olawoye, I. B.; Oluniyi, P. E.; Oguzie, J. U.; Uwanibe, J. N.; Kayode, T. A.; Olumade, T. J.; Ajogbasile, F. V.; Parker, E.; Eromon, P. E.; Abechi, P.; Fowotade, A.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.Item A 4-Year cross-sectional study of Hepatitis B virus infection among pregnant women: need for policy decision(Ecronicon, 2022-03) Fowotade, A.; Omoruyi, E. C.; Adesina, O.; Adekanmbi, O.; Adetunji, S.; Akande, K. O.; Adepoju, A.Background: The elimination of hepatitis B virus (HBV) in Nigeria, especially among pregnant women requires commitment from the government and health policy makers. This is predicated on comprehensive surveillance and epidemiological data. The objective of the current study is to provide the epidemiological data and unique perspectives that will inform accurate advocacy and influence policy decisions. Materials and Methods: A 4-year cross-sectional study was conducted among 2,428 consecutively recruited consenting pregnant women attending antenatal care at the University College Hospital, Ibadan, Oyo State, Nigeria. Venous blood was screened for HBsAg using Enzyme Linked Immunosorbent Assay (ELISA). HBsAg sero-negative samples were further tested for other HBV serological markers (anti-HBc, HBeAg and anti-HBe by ELISA. Socio-demographic and clinical details were obtained using a semi-structured questionnaire. Results: Overall HBsAg prevalence was 5.1% (2,305/2,482). Twenty three (1%) of the HBsAg sero-negative women tested positive to both anti-HBc and anti-HBe while 5.3% and 0.8% tested positive to only anti-HBc and anti-HBe, respectively. Additionally, 6.4% (38/594) of the HBV fully vaccinated pregnant women tested positive to HBsAg. Conclusion: Hepatitis B is endemic among Nigerian pregnant women. Serological patterns indicated possible occult hepatitis B infection. More political commitment from government and policy makers is urgently required.Item The african female Breast Cancer Epidemiology study protocol(Frontiers Media, 2022-04) Ezeome, E. R.; Yawe, K.-D. T.; Ayandipo, O.; Badejo, O.; Adebamowo, S. N.; Achusi, B.; Fowotade, A.; Ogun, G.; Adebamowo, C. A.Breast cancer is now the commonest cancer in most sub-Saharan African countries. Few studies of the epidemiology and genomics of breast cancer and its molecular subtypes in these countries have been done. The African Female Breast Cancer Epidemiology (AFBRECANE) study, a part of the Human Heredity and Health in Africa (H3Africa) initiative, is designed to study the genomics and epidemiology of breast cancer and its molecular subtypes in Nigerian women. We link recruitment of breast cancer cases at study sites with population-based cancer registries activities to enable ascertainment of the incidence of breast cancer and its molecular subtypes. We use centralized laboratory processing to characterize the histopathological and molecular diagnosis of breast cancer and its subtypes using multiple technologies. By combining genome-wide association study (GWAS) data from this study with that generated from 12,000 women participating in our prospective cohort study of cervical cancer, we conduct GWAS of breast cancer in an entirely indigenous African population. We test associations between dietary intakes and breast cancer and focus on vitamin D which we measure using dietary intakes, serum vitamin D, and Mendelian randomization. This paper describes the AFBRECANE project, its design, objectives and anticipated contributions to knowledge and understanding of breast cancer.Item The african female Breast Cancer Epidemiology study protocol(Frontiers Media, 2022-04) Ezeome, E. R.; Yawe, K.-D. T.; Ayandipo, O.; Badejo, O.; Adebamowo, S. N.; Achusi, B.; Fowotade, A.; Ogun, G.; Adebamowo, C. A.Breast cancer is now the commonest cancer in most sub-Saharan African countries. Few studies of the epidemiology and genomics of breast cancer and its molecular subtypes in these countries have been done. The African Female Breast Cancer Epidemiology (AFBRECANE) study, a part of the Human Heredity and Health in Africa (H3Africa) initiative, is designed to study the genomics and epidemiology of breast cancer and its molecular subtypes in Nigerian women. We link recruitment of breast cancer cases at study sites with population-based cancer registries activities to enable ascertainment of the incidence of breast cancer and its molecular subtypes. We use centralized laboratory processing to characterize the histopathological and molecular diagnosis of breast cancer and its subtypes using multiple technologies. By combining genome-wide association study (GWAS) data from this study with that generated from 12,000 women participating in our prospective cohort study of cervical cancer, we conduct GWAS of breast cancer in an entirely indigenous African population. We test associations between dietary intakes and breast cancer and focus on vitamin D which we measure using dietary intakes, serum vitamin D, and Mendelian randomization. This paper describes the AFBRECANE project, its design, objectives and anticipated contributions to knowledge and understanding of breast cancer.Item A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa(American Association for the Advancement of Science, 2021) Wilkinson, E.; Giovanetti, M.; Tegally, H.; San, J. E.; Lessells, R.; Cuadros, D.; Martin, D. P.; Rasmussen, D. A.; Zekri, A. N.; Fowotade, A.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.Item Patient care and clinical outcomes for patients with COVID-19 infection admitted to African high-care or intensive care units (ACCCOS): a multicentre, prospective, observational cohort study(Elsevier B.V., 2021) Biccard, B. M.; Gopalan, P. D.; Miller, M.; Michell, W. L.; Thomson, D.; Ademuyiwa, A.; Aniteye, E.; Calligaro, G.; Chaibou, M. S.; Dhufera, H. T.; Fowotade, A.Background There have been insufficient data for African patients with COVID-19 who are critically ill. The African COVID-19 Critical Care Outcomes Study (ACCCOS) aimed to determine which resources, comorbidities, and critical care interventions are associated with mortality in this patient population. Methods The ACCCOS study was a multicentre, prospective, observational cohort study in adults (aged 18 years or older) with suspected or confirmed COVID-19 infection who were referred to intensive care or high-care units in 64 hospitals in ten African countries (ie, Egypt, Ethiopia, Ghana, Kenya, Libya, Malawi, Mozambique, Niger, Nigeria, and South Africa). The primary outcome was in-hospital mortality censored at 30 days. We studied the factors (ie, human and facility resources, patient comorbidities, and critical care interventions) that were associated with mortality in these adult patients. This study is registered on ClinicalTrials.gov, NCT04367207. Findings From May to December, 2020, 6779 patients were referred to critical care. Of these, 3752 (55.3%) patients were admitted and 3140 (83.7%) patients from 64 hospitals in ten countries participated (mean age 55.6 years; 1890 [60.6%] of 3118 participants were male). The hospitals had a median of two intensivists (IQR 1–4) and pulse oximetry was available to all patients in 49 (86%) of 57 sites. In-hospital mortality within 30 days of admission was 48.2% (95% CI 46.4–50.0; 1483 of 3077 patients). Factors that were independently associated with mortality were increasing age per year (odds ratio 1.03; 1.02–1.04); HIV/AIDS (1.91; 1.31–2.79); diabetes (1.25; 1.01–1.56); chronic liver disease (3.48; 1.48–8.18); chronic kidney disease (1.89; 1.28–2.78); delay in admission due to a shortage of resources (2.14; 1.42–3.22); quick sequential organ failure assessment score at admission (for one factor [1.44; 1.01–2.04], for two factors [2.0; 1.33–2.99], and for three factors [3.66, 2.12–6.33]); respiratory support (high flow oxygenation [2.72; 1.46–5.08]; continuous positive airway pressure [3.93; 2.13–7.26]; invasive mechanical ventilation [15.27; 8.51–27.37]); cardiorespiratory arrest within 24 h of admission (4.43; 2.25–8.73); and vasopressor requirements (3.67; 2.77–4.86). Steroid therapy was associated with survival (0.55; 0.37–0.81). There was no difference in outcome associated with female sex (0.86; 0.69–1.06). Interpretation Mortality in critically ill patients with COVID-19 is higher in African countries than reported from studies done in Asia, Europe, North America, and South America. Increased mortality was associated with insufficient critical care resources, as well as the comorbidities of HIV/AIDS, diabetes, chronic liver disease, and kidney disease, and severity of organ dysfunction at admission.