There is a great demand for more rapid tests for SARS‐CoV‐2 detection to reduce waiting time, boost public health strategies for combating disease, decrease costs, and prevent overwhelming laboratory capacities. This study was conducted to assess the performance of 10 lateral flow device viral antigen immunoassays for the detection of SARS‐CoV‐2 in nasopharyngeal swab specimens. We analyzed 231 nasopharyngeal samples collected from October 2020 to December 2020, from suspected COVID‐19 cases and contacts of positive cases at Biotechnology Research Center laboratories, Tripoli, Libya. The performance of 10 COVID‐19 Antigen (Ag) rapid test devices for the detection of SARS‐CoV‐2 antigen was compared to a quantitative reverse transcription‐polymerase chain reaction (RT‐qPCR). In this study, 161 cases had symptoms consistent with COVID‐19. The mean duration from symptom onset was 6.6 ± 4.3 days. The median cycle threshold ( C t ) of positive samples was 25. Among the 108 positive samples detected by RT‐qPCR, the COVID‐19 antigen (Ag) tests detected 83 cases correctly. All rapid Ag test devices used in this study showed 100% specificity. While tests from six manufacturers had an overall sensitivity range from 75% to 100%, the remaining four tests had a sensitivity of 50%–71.43%. Sensitivity during the first 6 days of symptoms and in samples with high viral loads ( C t < 25), was 100% in all but two of the test platforms. False‐negative samples had a median C t of 34 and an average duration of onset of symptoms of 11.3 days (range = 5–20 days). Antigen test diagnosis has high sensitivity and specificity in early disease when patients present less than 7 days of symptom onset. Patients are encouraged to test as soon as they get COVID‐19‐related symptoms within 1 week and to seek medical advice within 24 h if they develop disturbed smell/taste. The use of rapid antigen tests is important for controlling the COVID‐19 pandemic and reducing the burden on molecular diagnostic laboratories.

The continuous emergence of new SARS-CoV-2 variants required rapid and reliable diagnostic methods for early detection and monitoring of the spread of the virus, especially in low-resource countries where whole genome sequencing is not available. We aimed to evaluate and compare the performance of two different RT-qPCR screening assays for the detection of B.1.617 lineage mutations. A total of 85 SARS-CoV-2 positive samples were collected between 9 th August and 10 September 2021 and screened by two mutation-specific RT-qPCR assays for simultaneous detection of B.1.617.1 and B.1.617.2 lineage mutations. VIASURE Variant II PCR assay identified 2 Delta variant-specific mutations (L452R, and P681 R) in 80% of tested samples, while the PKamp™ Variant Detect™ assay was only able to detect one Delta variant specific mutation (L452R) in 75% of tested samples. This is the first report to show the Delta variant as the cause of the third wave in Libya. The use of multiplex RT-qPCR assays has allowed the identification of new variants for rapid screening. However, RT-qPCR results should be confirmed by whole genome sequencing of SARS-COV-2.

A cluster-5 variant was detected in September 2020 in minks and humans in Denmark and currently classified as Alpha or B.1.1.7 strain. This variant presents several mutations in the spike region (S) which could increase the transmissibility of the virus 43-90% over previously circulating variants. The national center for disease control (NCDC) announced on 24th February 2021 the discovery of B.1.1.7 strain in Libya using a reverse-transcriptase PCR assay for S-gene target failure (SGTF) and reported that 25% of the tested samples were UK variant. This assay relies on the specific identification of the H69-V70 deletion in S gene which causes S gene drop out in RT-PCR; characteristic of the UK variant (B.1.1.7). This letter discusses our whole genome sequencing results of positive SARS-COV-2 samples with SGTF collected between 25th February - 4th March 2021 in Libya.

Background: There is a great demand for more rapid tests for SARS-COV-2 detection to reduce waiting time, boost public health strategies for combating disease, decrease costs, and prevent overwhelming laboratory capacities. This study was conducted to assess the performance of 10 antigen-based rapid assays for the detection of SARS-CoV-2 in nasopharyngeal swab specimens. Methods: We analyzed 231 nasopharyngeal samples collected from October 2020-December 2020, from suspected COVID-19 cases and contacts of positive cases at Biotechnology Research Center laboratories, Tripoli, Libya. The performance of 10 COVID-19 Ag rapid test devices (Fluorecare, ESPLINE, RapiGen, Abbott Panbio, Flowflex, Acon, Assut Europe, Orient Gene, CerTest, Bioperfectus, AMP) for the detection of SARS-CoV-2 antigen was compared to RT-qPCR. Results: Among the 108 positive samples detected by RT-qPCR, the COVID-19 antigen (Ag) tests detected 83, giving a sensitivity of 76.85% (95% CI, 67.75- 84.43). 161 patients were symptomatic. The median cycle threshold was 25. The mean duration from symptom onset was 6.6 plus/minus 4.3 days. Sensitivity and specificity during the first 6 days of symptoms and in samples with high viral loads ct<25, was 96.4%. No false positives were detected by any of the Ag tests utilized in this study. False negative samples had a median Ct of 34 and average duration of onset of symptoms of 11.3 days (range=5-20). Conclusions: Rapid antigen test diagnosis has high sensitivity and specificity in early disease when patients present less than 7 days of symptom onset. Patients are encouraged to test as soon as they get COVID-19 related symptoms within 1 week and to seek medical advice within 24 hrs. if they develop disturbed smell/taste. The use of rapid antigen tests is important for controlling COVID-19 pandemic and reducing burden on molecular diagnostic laboratories.