Anti-SARS-CoV-2 IgG antibodies after recovery from COVID-19 or vaccination in Libyan population: comparison of four vaccines (preprint)

Background: Natural and vaccine-induced immunity play an important role in controlling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Understanding humoral immunity to SARS-CoV-2 is of great importance for evaluating vaccine performance and inform public health decisions. Objective: We aimed to evaluate the level of IgG antibodies against SARS-CoV-2 and their persistence post infection or post-vaccination. Methods: A serological analysis (Immunoassay) to investigate the level of anti-spike IgG antibody responses following infection with SARS-CoV-2 or immunization with the first or second dose of the AstraZeneca, Sputnik, Sinovac and Sinopharm vaccines was performed. Results: A total of 9460 seropositive individuals were recruited. The mean levels of anti-spike IgG antibodies were higher in vaccinated participants with prior COVID-19 infections than in individuals without prior infection. Decline for IgG antibodies were faster in vaccinated individuals without previous COVID-19 infection compared to those with previous COVID-19 infection. Conclusion: A single dose of the vaccine is likely to provide greater protection against SARS-CoV-2 infection in subjects with prior SARS-CoV-2 infection, than in SARS-CoV-2-naive individuals. In addition, previous COVID-19 infection elicited robust and sustained levels of SARS-CoV-2 antibodies in vaccinated individuals.

COVID-19 Incidence in a Large Cohort of Hemodialysis Libyan Patients (preprint)

Hemodialysis patients are at a greater risk of severe disease from COVID-19. Of the 600 maintenance hemodialysis patients who were regular attendees at the Tripoli Hemodialysis Center in Tripoli, Libya, 12 patients contracted COVID-19 infection. Their ages ranged between 48 and 80 years, 3 of them were females (25%), and 4 (33.3%) had a history of contact with an infected person. The most common symptoms were fever (66.7%), dry cough (66.7%), dyspnea (91.7%) and fatigue (83.3%). Computed tomography of the chest showed radiological features of COVID-19 pneumonia, ground-glass opacities and consolidation in the lungs of all patients. Four of the patients died (33.3%). COVID-19 is a serious comorbidity for maintenance hemodialysis patients and is associated with a high mortality rate. Where no specific guidance for operation exist, guidelines should be developed or existing guidelines such as those of the CDC should be adapted to the local context.Funding: None to declare. Declaration of Interest: None to declare. Ethical Approval: Ethical approval was obtained from Bioethics Committee at BiotechnologyResearch Center (BEC-BTRC 18-2021).

Whole-genome sequencing of SARS-COV-2 reveals a substantially lower frequency of the UK variant than previously announced in Libya (preprint)

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.

Time scale performance of rapid antigen testing for SARS-COV-2: evaluation of ten rapid antigen assays (preprint)

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.