Abstract
The recently emerging coronavirus, severe acute respiratory syndrome coronavirus 2, (SARS-CoV-2) is the causative agent of the Coronavirus disease 2019 (COVID-19) pandemic. Since its discovery in the city of Wahan, China, SARS-CoV-2 has spread rapidly to invade all countries. In addition to its rapid transmission rate, it is characterized by high genetic mutation rates. The aim of this study is to provide an effective method for the isolation and propagation of SARS-CoV-2 in cell lines without any induction of genetic variations. In this study, we isolated SARS-CoV-2 from oro-nasopharyngeal swabs collected from Egyptian patients who were clinically diagnosed with COVID-19. Molecular identification of SARS-CoV-2 was performed by Real-Time Quantitative Reverse Transcription PCR (RT-qPCR). The isolated virus was propagated on Vero E6 cells without applying serial viral passages to avoid any variation of the viral genome. The replication and propagation were confirmed by the results of both RT-qPCR and the cytopathic effect (CPE). Moreover, SARS-CoV-2 was completely inactivated chemically using beta-propiolactone (βPL). Whole genome sequencing (WGS) of the propagated virus was performed in order to investigate mutational patterns. The genome sequences recovered in 2020 (n = 18) were similar to the reference strain, Wuhan-Hu-1, and were clustered as clade 20A. However, the genomic sequences recovered in 2021 (n = 2) were clustered as clade 21J. These two sequences are considered the first Delta (B.1.617.2) variants detected in Egypt. This study provides a reference for researchers in Egypt to isolate and propagate SARS-CoV-2 easily and efficiently. Furthermore, the prevalence of the SARS-CoV-2 delta variant in Egypt necessitates continuous monitoring of the efficacy of the applied treatment protocol and the effectiveness of current vaccines against such variants of concern (VOC).
Keywords: Delta variant; Isolation; Propagation; RT-qPCR; SARS-CoV-2; Variant of concern.
【저자키워드】 SARS-CoV-2, delta variant, RT-qPCR, Isolation, Variant of concern., Propagation, 【초록키워드】 COVID-19, coronavirus disease, Coronavirus disease 2019, Efficacy, Vaccine, coronavirus, pandemic, VoC, Variation, Genetic, variant, variants of concern, Delta, B.1.617.2, severe acute respiratory syndrome Coronavirus, delta variant, virus, continuous monitoring, Replication, Spread, Prevalence, China, RT-qPCR, Whole genome sequencing, PCR, nasopharyngeal swabs, qPCR, Patient, Treatment protocol, Effectiveness, clade, VERO E6 cells, Swab, Vero E6 cell, WGS, inactivated, CPE, Cytopathic effect, cell lines, genome sequence, Mutation rates, Genome sequences, Genetic variations, viral genome, Propagation, Vero E6, genetic mutation, causative agent, reference strain, acute respiratory syndrome, beta-propiolactone, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, city, sequence, passage, cell line, whole genome, transmission rate, genomic sequence, researcher, Wuhan-Hu-1, effective, collected, addition, clinically, applied, was performed, characterized, provide, diagnosed with COVID-19, the SARS-CoV-2, 【제목키워드】 molecular, COVID-19 patient, identification, SARS-CoV-2 delta,