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SARS-CoV-2 faecal negativity and gastrointestinal eubiosis in non-severe COVID-19 in Lagos, Nigeria

*Bamidele, T. A., Fowora, M. A., Raheem, T. Y., Ajayi, A., Adagbada, A., Yisau, J. I.,   Salau, O. Y., Shaibu, J. O., Amoo, O. S., Aiyedogbon, N., Fesobi, T. W.,          Akintunde, G., Iwalokun, B. A., Smith, S. I., and Salako, B. L. Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, 6, Edmund Crescent, Yaba-Lagos, Nigeria

*Correspondence to: bamideletj@gmail.com; Tel: +2348038578093; ORCID: https://orcid.org/0000–0003–2155–8639

 

Abstract:

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), when disseminated to the gastrointestinal tract (GIT), can cause alterations in the composition and diversity of the gastrointestinal tract microbiota. However, there is a paucity of data linking SARS-CoV-2 fecal negativity with the GI microbial balance. This study investigated the association between the GI bacterial composition and clinically defined asymptomatic, mild/moderate COVID-19 fecal-negative individuals.

Methodology: This was a cross sectional, comparative study of GI bacterial composition in COVID-19 nasopharyngeal (NP) -positive (n=7) and negative (n=5) participants at the testing facility of the Nigerian Institute of Medical Research between 6th July and 8th August 2022. Faecal samples were collected from the 12 participants. The RNA extracted from the NP-positive samples was used for RT‒qPCR detection of the nucleocapsid and open reading frame (ORF1ab) genes, while DNA from all the faecal samples was used for 16S rRNA metataxonomic analysis.      Continue reading “SARS-CoV-2 faecal negativity and gastrointestinal eubiosis in non-severe COVID-19 in Lagos, Nigeria”

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Detection of influenza virus by real-time polymerase chain reaction (RT-PCR) on archived COVID-19 respiratory specimens in Ibadan, Nigeria

*[1],[2]Ogunbode, J. O., ²Olatunji, O. A., and 1,2,3Fowotade, A.

¹Clinical Virology Unit, Department of Medical Microbiology and Parasitology, College of Medicine, University of Ibadan, Nigeria

²Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Nigeria

³Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Nigeria

*Correspondence to: oluyemijoseph8@gmail.com

Abstract:

Background: Every year, influenza virus affects millions of people, causing morbidity and mortality among adults and children prompting many to seek outpatient care. Influenza is largely undetected among infected individuals in lower-middle-income settings. Influenza co-infection with other respiratory viral infections is associated with a severe clinical presentation and a worse clinical outcome. The current study aimed to detect influenza A and B viruses from respiratory samples of patients with suspected CoVID-19, in order to establish possible co-infection, and its implications. Continue reading “Detection of influenza virus by real-time polymerase chain reaction (RT-PCR) on archived COVID-19 respiratory specimens in Ibadan, Nigeria”

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A mini-review of the global implications of the emerging SARS-CoV-2 XEC variant: Epidemiology, mutations, and mitigation strategies

1,2Ebede, S. O., 1,2Emeribe, S. C., 1,2Nwafia, I. N., 1,2Okeke, U. C., and *1,2Orabueze, I. N.

1Department of Medical Microbiology, Faculty of Basic Clinical Sciences, College of Medicine, University of Nigeria, Ituku-Ozalla Campus, Enugu, Nigeria

2Department of Microbiology, University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu, Nigeria*

Correspondence to: Iborabueze@gmail.com; ORCID: 0009-0005-8369-1568

Abstract:

The newly emerged SARS- CoV-2 XEC subvariant (XEC) is a global public health concern. Since its first detection in May 2024, it has spread rapidly to involve more than 45 countries globally. The World Health Organization and the Africa Centers for Disease Control and Prevention designated XEC a variant under monitoring (VUM), highlighting its global concern. XEC sub-variant is a descendant of the omicron lineage and a recombinant product of K.S.1.1 and KP3.3. Increased infectivity, enhanced immune evasion, and immune resistance, have been linked to specific spike protein mutations, S: F59S and S: T22N, alongside Apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 (APOBEC3)-driven mutations that facilitate immune escape and viral survival. Like its predecessor, the novel SARS-CoV-2 XEC variant exhibits flu-like symptoms. However, there is no evidence that it causes more severe illness than previously circulating Omicron variants. Nevertheless, the high reproduction number (Re) of the XEC variant suggests a higher chance of out competing the other major lineages. Wastewater surveillance has shown that XEC variant circulation is approximately 2 to 19 times higher than the number of cases that have been identified. This suggests that underreporting, decreased testing and declining genomic surveillance in many countries may be masking the true epidemiological burden of XEC. Mitigation strategies must prioritize mass vaccination campaigns, incorporating updated 2024-2025 vaccines and infection prevention and control measures. Sadly, vaccine hesitancy poses a significant challenge to the achievement of herd immunity. To address this, targeted public enlightenment campaigns are essential. Additionally, proactive and collaborative global efforts are necessary to curb the spread of emerging variants like XEC. Strengthened IPC practices, and sustained genomic surveillance will be critical in averting future waves and mitigating public health impacts. This review serves to provide insight into the XEC variant and call for action to prevent another looming pandemic. Continue reading “A mini-review of the global implications of the emerging SARS-CoV-2 XEC variant: Epidemiology, mutations, and mitigation strategies”

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COVID-19 and Dengue co-infection in paediatric patients: An endemic in a pandemic

†Pavani, S., †Srinath, M., Sultana, W., Rani, V. S., *Mehreen, S. F., and Ravi, V.

Viral Research and Diagnostic Laboratory, Department of Microbiology, Osmania Medical College, Koti, Hyderabad-500095, Telangana, India

*Correspondence to: drfakihamehreen@gmail.com; +91 8500499786

†Authors have equal contribution to the study

 

Abstract:

Background: The clinical presentation and outcome of COVID-19 are likely to be complicated by co-infection with other endemic viruses such as Dengue. This study aimed to investigate the occurrence of co-infections of SARS-CoV-2 and Dengue viruses in paediatric patients from Osmania General Hospital, Hyderabad, Telangana, during the COVID-19 pandemic. Continue reading “COVID-19 and Dengue co-infection in paediatric patients: An endemic in a pandemic”

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Comparative evaluation of automated KingFisher Flex Purification System 96 (ThermoFisher Scientific) and manual QIAamp Viral RNA Mini Kit (Qiagen) extraction methods for SARS-CoV-2

*[1]Zouré, A. A., 1Compaoré, T. R., 2Beré, J. A., 1Sagna, T., 1Soubeiga, S. T., 1Dabiré, C., 1Nikiema, A. R., 3Barro, N., and 1Ouedraogo, H. G.

1Department of Biomedical and Public Health, Institute of Health Sciences Research (IRSS/CNRST), 03 BP 7047 Ouagadougou 03, Burkina Faso

2Unité de Formation et de Recherche en Science et Technique (UFR/ST), Université Catholique de l’Afrique de l’Ouest Unité Universitaire à Bobo Dioulasso (UCAO/UUB)

3Laboratoire de Biologie Moléculaire, d’Epidémiologie et de Surveillance des Agents, Transmissibles par les

Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques Alimentaires et Nutritionnelles (CRSBAN),

Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso

*Correspondence to: abdouazaque@gmail.com; +22625363215; ORCiD: https://orcid.org/0000–0002–9423–024X

 

Abstract:

 Background: The extraction step of the viral material of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) influences the quality of reverse transcriptase-polymerase chain reaction (RT-PCR) results in diagnosis of coronavirus disease 2019 (COVID-19). The purpose of this cross-sectional study was to evaluate the diagnostic performance of the automated extraction system “KingFisher Flex Purification System 96 (ThermoFisher)” compared to the manual method with the “QIAamp Viral RNA Mini Kit (Qiagen)”.

Methodology: From October to December 2020, comparative diagnostic evaluation of two methods of SARSCoV-2 RNA extraction methods was conducted on 159 fresh and 120 frozen nasopharyngeal and oropharyngeal specimens collected from travellers and suspected cases or contacts of COVID-19 patients in Burkina Faso. The FastPlexTM Triplex 1-Step COVID 19 Detection Kit (RT-PCR, RNA extraction free) (Precigenome LLC) was used to amplify on the same PCR plate, RNA extracts from manual QIAamp Viral RNA Mini Kit and automated KingFisher Flex Purification System 96 (ThermoFisher) using the QuantStudio5 thermal cycler (Applied Biosystems). Analysis of the diagnostic performance of the SARS-CoV-2 RT-PCR assay following RNA extraction by the two methods was done using an online OpenEpi software. Continue reading “Comparative evaluation of automated KingFisher Flex Purification System 96 (ThermoFisher Scientific) and manual QIAamp Viral RNA Mini Kit (Qiagen) extraction methods for SARS-CoV-2”

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Prevalence of COVID-19 at the Wahgnion-Gold mining site in Burkina Faso and use of RT-PCR initial cycle threshold to monitor the dynamics of SARS-CoV-2 load

+1Cissé, A., +*1,2Lingani, M., 1Tao, M., 1Nana, S., 1Kaboré, B., 3Eric D. A. S., 4Nassouri, A., 1Diagbouga, S., 5Bamba, S., and 1Tarnagda, Z.

1National Influenza Reference Laboratory, Unité des Maladies à Potentiel Epidémique, Maladies Émergentes et

Zoonoses, Institut de Recherche en Sciences de la Santé, Burkina Faso

2Unité de Recherche Clinique de Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso

3Teranga Gold Corporation, Ouagadougou, Burkina Faso

4Wahgnion Gold Operation, Ouagadougou, Burkina Faso

5Institut Supérieur des Sciences de la Santé, Université Nazi BONI, Bobo-Dioulasso, Burkina Faso

*Correspondence to: lingani10@yahoo.fr; +joint first authors

 

Abstract:

 Background: To control the spread of coronavirus disease-19 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), it is necessary to adequately identify and isolate infectious patients particularly at the work place. Real time polymerase chain reaction (RT-PCR) assay is the recommended confirmatory method for the diagnosis of SARS-CoV-2 infection. The aim of this study was to determine the prevalence of SARSCoV-2 infection in Burkina Faso and to use the initial cycle threshold (Ct) values of RT-PCR as a tool to monitor the dynamics of the viral load.

Methodology: Between September 2021 and February 2022, oropharyngeal and/or nasopharyngeal swab samples of consecutively selected COVID-19 symptomatic and apparently healthy workers from the Wahgnion mining site in the South-western Burkina Faso who consented to the study were collected according to the two weeks shift program and tested for SARS-CoV-2 using RT-PCR assay. Patients positive for the virus were followed-up weekly until tests were negative. Association of the initial RT-PCR Ct values with disease duration was assessed by adjusted linear regression approach. Two-sided p value < 0.05 was considered statistically significant. Continue reading “Prevalence of COVID-19 at the Wahgnion-Gold mining site in Burkina Faso and use of RT-PCR initial cycle threshold to monitor the dynamics of SARS-CoV-2 load”

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Evolution of SARS-CoV-2 variants: a mini-review

1Musa-Booth, T. O., *2Adegboro, B., and 2Medugu, N.
11928 Woodlawn Drive, Woodlawn, Maryland 21207, USA

2Department of Medical Microbiology and Immunology, Nile University of Nigeria, Abuja, Nigeria

*Correspondence to: boazadegboro@gmail.com; boaz.adegboro@nileuniversity.edu.ng

Abstract:

SARS-CoV-2 has evolved over time with several mutations, especially on the spike protein, which has led to emergence of various variants. With the evolution of SARS-CoV-2 come new challenges in surveillance, effectiveness of preventive and treatment strategies, and outcome of the disease. Despite the lockdowns, mask mandates and other preventive measures put in place, in addition to over 10 million vaccine doses that have been administered globally as of February 2022, COVID-19 cases have risen to over 435 million and resulted in over 5.9 million deaths, largely as a result of the evolution of SARS-CoV-2 variants. To review the evolution of these variants, we searched different online database sources using keywords such as “source of SARS-CoV-2”, “SARS-CoV-2 origin”, “evolution of SARS-CoV-2”, “SARS-CoV-2 variants”, “variants of concern”, “variants of interest”, and “variants of high consequence”. This was to enable us give a good report about the various variants of SARS-CoV-2 that have emerged so far, and the public health challenges posed by them. Continue reading “Evolution of SARS-CoV-2 variants: a mini-review”

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Pathologic changes in patients infected with SARS-CoV-2: a review

*1Babazhitsu, M., 2Adegoke, O. O., 3Abayomi, S. A., and 4Adegboro, B.

1Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Sokoto State, Nigeria 2Department of Pathology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Nigeria 3Department of Medical Microbiology and Parasitology, LAUTECH Teaching Hospital, Ogbomoso, Nigeria 4Department of Medical Microbiology and Immunology, Nile University of Nigeria, Abuja

*Correspondence to: babazhitsu.makun@udusok.edu.ng; +234 8032874925

Abstract:
Severe acute respiratory syndrome–coronavirus-2 (SARS-CoV-2) enters cells using the angiotensin converting enzyme 2 (ACE2), which are expressed by the respiratory tract endothelium, epithelial cells of the stomach, duodenum, ileum, rectum, cholangiocytes, and hepatocytes. Pathological examinations of these organs are not feasible method of diagnosis but can explain pathological changes, pathogenesis of the disease, and the cause of death in COVID-19 cases. In this review, we performed a literature search for COVID-19-related pathological changes seen during post-mortem examinations in different organs of the body including the lungs, gastrointestinal tract, liver, kidney, skin, heart and blood. Our findings showed that SARS-CoV-2 has damaging effects on many organs, probably due to the host immune responses to the presence of the virus. It is recommended that both antiviral and immunomodulatory agents should be considered in the management of COVID-19 patients for better prognosis, and clinical outcome. Continue reading “Pathologic changes in patients infected with SARS-CoV-2: a review”

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A review of the possible prognostic values of biochemical changes in patients with SARS-CoV-2 infections

*1Adegboro, B., 2Babazhitsu, M., and 3Mba, N. I.

Departments of 1Medical Microbiology and Immunology, and 3Chemical Pathology, Nile University of Nigeria, Abuja 2Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria

*Correspondence to: boazadegboro@gmail.com; boaz.adegboro@nileuniversity.edu.ng

Abstract:
Because of high mortality and long-term hospital stay among patients with SARS-CoV-2 infections, it is important to search for biochemical changes in different organs and systems that could be useful in diagnosis and prognosis of COVID-19. We conducted a literature search of online databases including PubMed, Web of Science, Scopus and Google scholar for relevant materials on biochemical changes in SARS-COV-2 infections published between December 2019 and March 2021. The review shows that SARS-COV-2 uses the angiotensin converting enzyme 2 (ACE2) for attachment and entry into host cells. These ACE2 are abundantly expressed by the epithelial cells of the respiratory tract and moderately expressed by the epithelial cells of the esophagus, stomach, duodenum, ileum, rectum, cholangiocytes, liver hepatocytes, pancreatic beta cells, and kidney tubular cells. This explains the systemic nature of SARS-COV-2 infection, and the high morbidity and mortality associated with COVID-19. Although, tests to assess biochemical changes are not specific enough for the diagnosis of SARS-CoV-2 infection, they may be useful for predicting outcome of COVID-19. This review highlights biochemical parameters that are significantly elevated or reduced in SARS-COV-2 infections, and which can be used as predictive factors of the severity and prognosis in COVID-19 patients. Continue reading “A review of the possible prognostic values of biochemical changes in patients with SARS-CoV-2 infections”

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Africa’s COVID-19 story: cheap innovation technology and climate protective effect to her rescue?

*Adesokan, A., and MacLean, M.

PreciseMed 272 Bath Street, Glasgow, G2 4JR Scotland

*Correspondence to: dapoadesokan@gmail.com; Ade@precisemed.co.uk

Abstract:
As the COVID-19 pandemic sweeps the globe, causing tens of thousands of deaths in most Western countries with economies round the world in turmoil, Africa has so far been largely spared the kind of impact that has thrown the United States, South America and Europe into crisis. Most African countries remain seriously unprepared to handle the pandemic of the nature the Western world is dealing with; Africa, from Mali to Ethiopia to Libya and down to South Africa, have insufficient ventilators or intensive care beds to cope with COVID-19 should it strike with ferocity as it is doing in the Western world. As COVID-19 reaches the shores of Africa, despite poor health facilities, poor living conditions and inadequate availability of clean water across the continent, Africans are still putting up a fight taking COVID-19 head on with use of cheap technology, and help from the continent’s protective climate. However, Africa cannot afford to be complacent. African countries must continue to adopt strict social distancing measures, educate their people on the importance of intake of regular vitamin D, good exercising habit, good sleep pattern, adequate hand hygiene measures, as well as strictly enforcing the “test, trace and isolate“ model to the letter for the continent to take on the fight head on and wage a proper war against COVID-19. Continue reading “Africa’s COVID-19 story: cheap innovation technology and climate protective effect to her rescue?”