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2.
Microbiol Spectr ; 9(2): e0068021, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1455680

ABSTRACT

Validated assays are essential for reliable serosurveys; however, most SARS-CoV-2 immunoassays have been validated using specimens from China, Europe, or U.S. populations. We evaluated the performance of five commercial SARS-CoV-2 immunoassays to inform their use in serosurveys in Nigeria. Four semiquantitative enzyme-linked immunosorbent assays (ELISAs) (Euroimmun anti-SARS-CoV-2 nucleocapsid protein [NCP] immunoglobulin G [IgG], Euroimmun spike SARS-CoV-2 IgG, Mologic Omega COVID-19 IgG, Bio-Rad Platelia SARS-CoV-2 Total Ab) and one chemiluminescent microparticle immunoassay (Abbott Architect SARS-CoV-2 IgG) were evaluated. We estimated the analytical performance characteristics using plasma from 100 SARS-CoV-2 PCR-positive patients from varied time points post-PCR confirmation and 100 prepandemic samples (50 HIV positive and 50 hepatitis B positive). The Bio-Rad assay failed the manufacturer-specified validation steps. The Euroimmun NCP, Euroimmun spike, and Mologic assays had sensitivities of 73.7%, 74.4%, and 76.9%, respectively, on samples taken 15 to 58 days after PCR confirmation and specificities of 97%, 100%, and 83.8%, respectively. The Abbott assay had 71.3% sensitivity and 100% specificity on the same panel. Parallel or serial algorithms combining two tests did not substantially improve the sensitivity or specificity. Our results showed lower sensitivity and, for one immunoassay, lower specificity compared to the manufacturers' results and other reported validations. Seroprevalence estimates using these assays might need to be interpreted with caution in Nigeria and similar settings. These findings highlight the importance of in-country validations of SARS-CoV-2 serological assays prior to use to ensure that accurate results are available for public health decision-making to control the COVID-19 pandemic in Africa. IMPORTANCE This study used positive and negative sample panels from Nigeria to test the performance of several commercially available SARS-CoV-2 serological assays. Using these prepandemic and SARS-CoV-2-positive samples, we found much lower levels of sensitivity in four commercially available assays than most assay manufacturer reports and independent evaluations. The use of these assays with suboptimal sensitivity and specificity in Nigeria or countries with population exposure to similar endemic pathogens could lead to a biased estimate of the seroprevalence, over- or underestimating the true disease prevalence, and limit efforts to stop the spread of SARS-CoV-2. It is important to conduct in-country validations of serological SARS-CoV-2 assays prior to their widespread use, especially in countries with limited representation in published assay validations.


Subject(s)
Antibodies, Viral/blood , COVID-19/diagnosis , Coronavirus Nucleocapsid Proteins/immunology , Immunoglobulin G/blood , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Adult , COVID-19/epidemiology , Enzyme-Linked Immunosorbent Assay/methods , Female , Humans , Male , Nigeria/epidemiology , Phosphoproteins/immunology , Sensitivity and Specificity , Seroepidemiologic Studies
3.
PLoS One ; 16(6): e0252611, 2021.
Article in English | MEDLINE | ID: covidwho-1264216

ABSTRACT

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.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , RNA, Viral/analysis , SARS-CoV-2/isolation & purification , Adolescent , Adult , Aged , COVID-19/blood , COVID-19/epidemiology , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Nigeria/epidemiology , RNA, Viral/blood , RNA, Viral/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity , Young Adult
4.
Heliyon ; 7(5): e07100, 2021 May.
Article in English | MEDLINE | ID: covidwho-1233440

ABSTRACT

The SARS-CoV-2 virus is highly infectious resulting in increased infection and death among the front-line Healthcare Workers (HCW) because of limited access to personal protective equipment (PPE). This study assesses the availability and self-reported use of PPE amongst HCW during the COVID-19 pandemic in Nigeria. A mixed-method study was conducted through a cross-sectional survey and in-depth interviews amongst HCW. Quantitative data analysis was done using SPSS version 26 and thematic analysis was done for the in-depth interview. A total of 258 HCW completed the survey while 15 HCW took part in the in-depth interview. The mean age was 40 (±8.6) years, 67.4% were female and 83.3% were married. 49% were Doctors, 21.1% were Nurses, 28.7% were other allied HCW and 62.2% had at least 10 years of practice experience. Only 22.1% of HCWs had regular access to PPE and only 20.6% had access to N-95 facemask compare to other PPEs. Male HCWs and those working at secondary or tertiary facilities had access to N-95 facemask (p-value 0.025 and 0.010 respectively). The facilitator of PPE use is leadership quality of hospital head and donation of PPE to the facilities while the barriers to PPE use include a limited supply of PPE, as well as facility's infrastructural and operational challenges. The study reported limited access to essential PPE with varying perspectives on its use. Therefore, access, knowledge, and appropriate use of PPE need urgent attention with improved implementation of infection control policy at the facility level.

5.
PLoS One ; 16(2): e0246637, 2021.
Article in English | MEDLINE | ID: covidwho-1063224

ABSTRACT

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.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , RNA, Viral/genetics , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/virology , Humans , Nigeria/epidemiology , RNA, Viral/analysis , Retrospective Studies , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
6.
PLoS One ; 16(1): e0243271, 2021.
Article in English | MEDLINE | ID: covidwho-1024411

ABSTRACT

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.


Subject(s)
COVID-19/virology , SARS-CoV-2/genetics , Base Sequence , COVID-19/epidemiology , Genome, Viral , High-Throughput Nucleotide Sequencing , Humans , Nigeria/epidemiology , Phylogeny , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction
7.
Pan Afr Med J ; 35(Suppl 2): 107, 2020.
Article in English | MEDLINE | ID: covidwho-962474

ABSTRACT

Introduction: effective and safe means of sample collection is a crucial component of testing for Covid-19. Uptake of testing is key to containing and controlling the spread of the virus. Scientists have been working on various strategies that will increase the uptake of testing for COVID-19. One such method involves the use of the drive-through sampling strategy. Methods: data was collected by both qualitative and quantitative methods. An eligibility form was filled online. While in-depth interviews were conducted for the qualitative aspect of the study. Results: 2,600 visits were recorded at the website, 2300 (88.46%) participants successfully registered for the test. 57.4% were found eligible of which 78.0% presented for the test. This Consisted of 78.0% drive-through and 22.0% walk-in. The average time for transiting through the drive-through site was 19.2 ± 4.6minutes while that of the walk-in was 28 ± 9.2min. This difference was statistically significant (p<0.001). In the qualitative component, respondents opined that maximum safety measures were deployed to protect both participants and health workers. Most said that the turnaround time for the sampling process was short. Conclusion: the sampling strategy although largely successful, is largely dependent on Internet penetrability, thus this sampling modality will be best utilized as an adjunct to established models of sample collection.


Subject(s)
COVID-19 Testing/statistics & numerical data , COVID-19/diagnosis , SARS-CoV-2 , COVID-19/prevention & control , Humans , Interviews as Topic , Nigeria , Specimen Handling
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