Towards preliminary inactivated vaccine for SARS CoV-2 isolated from Egypt: ‎Isolation, propagation and inactivation of SARS CoV-2 Omicron variant (in vitro ‎study)‎

Document Type : Original Article


1 Biological Prevention ‎Department, Egypt Army, ‎Egypt

2 Biological Prevention Department, Egypt Army, Egypt

3 Botany and Microbiology ‎Department, Faculty of ‎Science, Benha University, ‎Egypt

4 Botany and Microbiology ‎Department, Faculty of ‎Science, Suez Canal ‎University, Egypt‎


Background: The primary causative agent of the COVID-19 pandemic is the newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). After being identified in the Chinese city of Wuhan, SARS-CoV-2 quickly spread to every country worldwide. The highly mutated SARS-CoV-2 variant B.1.1.529 (Omicron) has the ability to evade the neutralizing antibodies produced by vaccines. This is because the immune response generated by the vaccines is focused on a specific group of receptor-binding domain (RBD) epitopes. The objective of this work is to establish a systematic protocol for isolating, cultivating, and inactivating the SARS-CoV-2 Omicron variant in cell lines without causing any genetic alterations. This is done to develop an inactivated vaccine and make it ready for future pre-clinical trials in animal models. Material and methods: This investigation involves the collection of nasopharyngeal swabs (n = 40) from individuals who are suspected to have COVID-19. The molecular identification of SARS-CoV-2 was achieved by Real-Time Quantitative Reverse Transcription PCR (RT-qPCR). Whole genome sequencing (WGS) has been performed for all collected samples (n = 40). The determination of clade assignment, Pangolin lineages, mutation calling, and phylogenetic placement was performed. We selected only one sample for our candidate vaccine, which has the lowest Ct value and represents the most common strain among all the collected samples. The selected virus sample was cultured on the Vero cell line for 7 continuous passages. The confirmation of SARS CoV-2 propagation was based on the data obtained from both RT-qPCR and the observation of cytopathic effect (CPE). The tissue culture infective dose 50% (TCID50) was determined to examine the growth kinetics for each passage in the tissue culture. The genetic stability of our selected sample for the vaccine candidate was investigated by performing whole genome sequencing (WGS) of the propagated virus. Furthermore, SARS-CoV-2 was fully inactivated by chemical means utilizing beta-propiolactone (βPL), and the overall protein content was assessed. Result: Finally, we will possess a genetically consistent, inactivated form of the SARS CoV-2 Omicron variant, specifically clade 22B and Pango lineage BA.5.2.  Conclusion: This inactivated variant will have a known titer and total protein content, making it suitable for further examination in a pre-clinical study aimed at creating an inactivated vaccine for the SARS CoV-2 Omicron variant that was isolated in Egypt.


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