Comparative performance of SARS-CoV-2 real-time PCR diagnostic assays on samples from Lagos, Nigeria.

A key element in containing the spread of the SARS-CoV-2 infection is quality diagnostics which is affected by several factors. We now report the comparative performance of five real-time diagnostic assays. Nasopharyngeal swab samples were obtained from persons seeking a diagnosis for SARS-CoV-2 infection in Lagos, Nigeria. The comparison was performed on the same negative, low, and high-positive sample set, with viral RNA extracted using the Qiagen Viral RNA Kit. All five assays are one-step reverse transcriptase real-time PCR assays. Testing was done according to each assay's manufacturer instructions for use using real-time PCR platforms. 63 samples were tested using the five qPCR assays, comprising of 15 negative samples, 15 positive samples (Ct = 16-30; one Ct = 35), and 33 samples with Tib MolBiol E-gene Ct value ranging from 36-41. All assays detected all high positive samples correctly. Three assays correctly identified all negative samples while two assays each failed to correctly identify one different negative sample. The consistent detection of positive samples at different Ct/Cq values gives an indication of when to repeat testing and/or establish more stringent in-house cut-off value. The varied performance of different diagnostic assays, mostly with emergency use approvals, for a novel virus is expected. Comparative assays' performance reported may guide laboratories to determine both their repeat testing Ct/Cq range and/or cut-off value.

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.

COVID-19 Pandemic: A Case for Phytomedicines.

Coronavirus disease 2019 (COVID-19) is an infection caused by a newly discovered coronavirus which was identified in Wuhan, China. The race is on globally to repurpose drugs for COVID-19 and develop a safe and effective vaccine against the disease. There is an urgent need to search for effective remedies against COVID-19 from the rich and extensive flora of Africa and the world. A literature search was conducted to obtain information on drugs with the potential for effectiveness in the treatment of COVID-19 based mostly on outcomes of preclinical studies and a few clinical investigations. This was considered important to this perspective as some of the identified mechanisms of action may be related to potential anti-COVID-19 actions of phytomedicines. The findings from the literature search were also used to establish the need for exploration of phytomedicines in the fight against COVID-19. This perspective identifies the need to preserve the rich tradition of herbal medicine in Africa, repositioning it by inculcating all aspects of discovery, development, and chemical evaluation of pharmaceuticals from medicinal plants for effective management of prevalent diseases. The identified mechanisms of action of current drugs under consideration for the treatment of COVID-19 include preventing fusion of SARS-CoV-2 with human cells; decrease acidity in endosomes, cell membrane-derived vesicles for transportation of the virus within the host cell and within which the virus can replicate; and blockade of the production of proinflammatory cytokines. Phytomedicines may possibly elicit either one or a combination of these effects. The case for the exploration of phytomedicines against COVID-19 is strengthened by the emergence of a number of conventional drugs from medicinal plants and the emergence of botanicals with proven efficacy for some medical conditions. Caution against indiscriminate use of medicinal plants in the guise of treating COVID-19 has been highlighted and the need for reliable preclinical and clinical studies.

Molecular confirmation and phylogeny of Lassa fever virus in Benin Republic 2014-2016.

BACKGROUND: The changing epidemiology of the Lassa virus from endemic areas to other parts of West Africa has been reported. However, there have been no documented Lassa fever transmission chains in the Benin Republic. Two outbreaks of Lassa fever (November 2014 and January 2016) in the Benin Republic were characterised by a high number of deaths (more than 50%) among 27 confirmed and other unconfirmed cases. OBJECTIVES: We report the detection, confirmation and relatedness of the Lassa virus strains from the Benin Republic with other isolates within the West African Sub-region. METHODS: A total of 70 blood samples (16 from 2014 and 54 from 2016) from suspected cases with signs and symptoms suggestive of viral haemorrhagic fever were received for molecular analysis at the Centre for Human and Zoonotic Virology, College of Medicine, University of Lagos and the Lagos University Teaching Hospital. With the detection of the Lassa virus RNA by reverse transcriptase polymerase chain reaction, sequencing and phylogenetic analyses were performed using the Sanger dideoxy sequencing technology platform and the MEGA6 software. RESULTS: S segments of the Lassa virus RNA genome were detected in 5 (7.1%) of the 70 samples analysed. Sequencing and a phylogenetic tree construction confirmed that the strain of Lassa virus had close relationships with strains previously isolated from Nigeria. CONCLUSION: We confirmed the presence of the Lassa virus in the Benin Republic, with 2 strains having molecular epidemiological links with Lineage I and II strains from Nigeria. To reduce the likelihood of outbreaks, there is a need for heightened awareness and strengthened surveillance systems about Lassa fever, particularly in the sub-region.

Biosafety level-2 laboratory diagnosis of Zaire Ebola virus disease imported from Liberia to Nigeria.

INTRODUCTION: Global travel is an efficient route of transmission for highly infectious pathogens and increases the chances of such pathogens moving from high disease-endemic areas to new regions. We describe the rapid and safe identification of the first imported case of Ebola virus disease in a traveler to Lagos, Nigeria, using conventional reverse transcription polymerase chain reaction (RT-PCR) in a biosafety level (BSL)-2 facility. CASE PRESENTATION: On 20 July 2014, a traveler arrived from Liberia at Lagos International Airport and was admitted to a private hospital in Lagos, with clinical suspicion of Ebola virus disease. METHODOLOGY AND OUTCOME: Blood and urine specimens were collected, transported to the Virology Unit Laboratory at the College of Medicine, University of Lagos, and processed under stringent biosafety conditions for viral RNA extraction. RT-PCR was set-up to query the Ebola, Lassa and Dengue fever viruses. Amplicons for pan-filoviruses were detected as 300 bp bands on a 1.5% agarose gel image; there were no detectable bands for Lassa and Dengue viral RNA. Nucleotide BLAST and phylogenetic analysis of sequence data of the RNA-dependent RNA polymerase (L) gene confirmed the sequence to be Zaire ebolavirus (EBOV/Hsap/NGA/2014/LIB-NIG 01072014; Genbank: KM251803.1). CONCLUSION: Our BSL-2 facility in Lagos, Nigeria, was able to safely detect Ebola virus disease using molecular techniques, supporting the reliability of molecular detection of highly infectious viral pathogens under stringent safety guidelines in BSL-2 laboratories. This is a significant lesson for the many under-facilitated laboratories in resource-limited settings, as is predominantly found in sub-Saharan Africa.

Experience of quality management system in a clinical laboratory in Nigeria.

ISSUES: Quality-management systems (QMS) are uncommon in clinical laboratories in Nigeria, and until recently, none of the nation's 5 349 clinical laboratories have been able to attain the certifications necessary to begin the process of attaining international accreditation. Nigeria's Human Virology Laboratory (HVL), however, began implementation of a QMS in 2006, and in 2008 it was determined that the laboratory conformed to the requirements of ISO 9001:2000 (now 2008), making it the first diagnostic laboratory to be certified in Nigeria. The HVL has now applied for the World Health Organization (WHO) accreditation preparedness scheme. The experience of the QMS implementation process and the lessons learned therein are shared here. DESCRIPTION: In 2005, two personnel from the HVL spent time studying quality systems in a certified clinical laboratory in Dakar, Senegal. Following this peer-to-peer technical assistance, several training sessions were undertaken by HVL staff, a baseline assessment was conducted, and processes were established. The HVL has monitored its quality indicators and conducted internal and external audits; these analyses (from 2007 to 2009) are presented herein. LESSONS LEARNED: Although there was improvement in the pre-analytical and analytical indicators analysed and although data-entry errors decreased in the post-analytical process, the delay in returning laboratory test results increased significantly. There were several factors identified as causes for this delay and all of these have now been addressed except for an identified need for automation of some high-volume assays (currently being negotiated). Internal and external audits showed a trend of increasing non-conformities which could be the result of personnel simply becoming lax over time. Application for laboratory accreditation, however, could provide the renewed vigour needed to correct these non-conformities. RECOMMENDATION: This experience shows that sustainability of the QMS at present is a cause for concern. However, the tiered system of accreditation being developed by WHO-Afro may act as a driving force to preserve the spirit of continual improvement.

Experience of quality management system in a clinical laboratory in Nigeria

Issues: Quality-management systems (QMS) are uncommon in clinical laboratories in Nigeria; and until recently; none of the nation's 5 349 clinical laboratories have been able to attain the certifications necessary to begin the process of attaining international accreditation. Nigeria's Human Virology Laboratory (HVL); however; began implementation of a QMS in 2006; and in 2008 it was determined that the laboratory conformed to the requirements of ISO 9001:2000 (now 2008); making it the first diagnostic laboratory to be certified in Nigeria. The HVL has now applied for the World Health Organization (WHO) accreditation preparedness scheme. The experience of the QMS implementation process and the lessons learned there in are shared here. Description: In 2005; two personnel from the HVL spent time studying quality systems in a certified clinical laboratory in Dakar; Senegal. Following this peer-to-peer technical assistance; several training sessions were undertaken by HVL staff; a baseline assessment was conducted; and processes were established. The HVL has monitored its quality indicators and conducted internal and external audits; these analyses (from 2007 to 2009) are presented herein. Lessons learned: Although there was improvement in the pre-analytical and analytical indicators analysed and although data-entry errors decreased in the post-analytical process; the delay in returning laboratory test results increased significantly. There were several factors identified as causes for this delay and all of these have now been addressed except for an identified need for automation of some high-volume assays (currently being negotiated). Internal and external audits showed a trend of increasing non-conformities which could be the result of personnel simply becoming lax over time. Application for laboratory accreditation; however; could provide the renewed vigour needed to correct these non conformities. Recommendation: This experience shows that sustainability of the QMS at present is a cause for concern. However; the tiered system of accreditation being developed by WHO-Afro may act as a driving force to preserve the spirit of continual improvement

Effect of HIV-1 infection and increasing immunosuppression on menstrual function.

AIM: The aim of this study was to determine the prevalence, pattern and determinants of menstrual abnormalities in HIV-positive Nigerian women. METHODS: A cross-sectional study was carried out involving 3473 (2549 HIV-seropositive and 924 seronegative) consecutive and consenting women seen at the HIV treatment centers at the Nigerian Institute of Medical Research, Lagos and the Federal Medical Centre, Markurdi. RESULTS: The sociodemographic characteristics of the two groups were comparable, except for body mass index (BMI): the HIV-negative women (28.1 ± 8.1) had statistically significantly (P < 0.005) higher BMI compared to the HIV-positive women (21.9 ± 7.5). Menstrual abnormalities were significantly more common in women living with HIV/AIDS (29.1%) compared to the HIV-negative (18.9%) women (P < 0.001). The proportions of women in the two groups with intermenstrual bleeding, menorrhagia, hypermenorrhea, and postcoital bleeding were similar (P > 0.005), however amenorrhea, oligomenorrhea, irregular periods and secondary dysmenorrhea were more common in the HIV-positive women (P < 0.02). Primary dysmenorrhea was less common in HIV-positive women (P < 0.03). Among the HIV-positive women, menstrual dysfunction was more common in women living with HIV/AIDS with opportunistic infections, CD4 count < 200, not undertaking therapy, symptomatic disease and BMI < 20. However, after controlling for cofounders, only CD4 < 200 (odds ratio [OR], 3.65; 95% confidence interval [CI], 1.2-9.7), BMI < 20 (OR, 2.4; 95%CI, 1.3-3.5) and not taking antiretroviral drugs (OR, 2.05; CI, 1.7-6.5) were associated with amenorrhea, oligomenorrhea, irregular periods and secondary dysmenorrhea. CONCLUSION: HIV-positive women in this study experienced more menstrual abnormalities of amenorrhea, oligomenorrhea, and irregular periods compared to the HIV-negative controls. HIV-positive women with CD4 count < 200, BMI < 20 and who do not take antiretroviral drugs are at the greatest risk.