Detection of SARS-CoV-2 B.1.1.529 (Omicron) variant by SYBR Green-based RT-qPCR (preprint)

Background: The COVID-19 pandemic is unceasingly spreading across the globe, and recently a highly transmissible Omicron SARS-CoV-2 variant (B.1.1.529) has been discovered in South Africa and Botswana. Rapid identification of this variant is essential for pandemic assessment and containment. However, variant identification is mainly being performed using expensive and time-consuming genomic sequencing. Methods and results: In this study we propose an alternative RT-qPCR approach for the detection of the Omicron BA.1 variant using a low-cost and rapid SYBR Green method. We have designed specific primers to confirm the deletion mutations in the spike (S {triangleup}143-145) and the nucleocapsid (N {triangleup}31-33) which are characteristics of this variant. For the evaluation, we used 120 clinical samples from patients with PCR-con[fi]rmed SARS-CoV-2 infections, and displaying an S-gene target failure (SGTF) when using TaqPath COVID-19 kit (Thermo Fisher Scientific, Waltham, USA) that included the ORF1ab, S, and N gene targets. Our results showed that all the 120 samples harbored S {triangleup}143-145 and N {triangleup}31-33, which was further confirmed by Whole genome sequencing (WGS) of 4 samples thereby validating our SYBR Green-based protocol. Conclusions: This protocol can be easily implemented to rapidly confirm the diagnosis of the Omicron BA.1 variant in COVID-19 patients and prevent its spread among populations, especially in countries with high prevalence of SGTF profile.

Remdesivir Treatment alters Circulating MicroRNA Profile in Coronavirus Disease 2019 (COVID-19) Patients (preprint)

Coronavirus disease 2019 (COVID-19), a serious infectious disease caused by the newly discovered Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), represents a significant global health crisis nowadays. Although no specific antiviral drug has been proven to be fully effective against COVID-19, Remdesivir (GS-5734), a nucleoside analogue prodrug, showed beneficial effects upon treating severe hospitalized COVID-19 cases. The molecular mechanism underlying this beneficial therapeutic effect is still vague. In this study, we assessed the effect of Remdesivir treatment on the signature of circulating miRNAs in the plasma of COVID-19 patients. MiRCURY LNA miRNome qPCR Panels were used to characterize the miRNA signature. Individual quantitative real-time RT-PCR (qRT-PCR) was performed to confirm the outcome of miRCURY LNA miRNome qPCR Panels. Our results revealed that Remdesivir can restore the expression of a panel of miRNAs being upregulated in COVID-19 patients into levels comparable to those exhibited by healthy donors. Bioinformatics analysis revealed that these miRNAs are involved in diverse biological processes such as Transforming growth factor beta (TGF-β) signalling pathway, Hippo signaling, P53 signalling and Rap1 signaling pathway. On the other hand, 3 miRNAs (hsa-miR-7-5p, hsa-miR-10b-5p, hsa-miR-130b-3p) were upregulated in patients only following Remdesivir treatment or in naturally remitted patients. These upregulated miRNAs could serve as biomarkers of COVID-19 remission. The output of this study highlights that Remedisivir therapeutic potential involves miRNA-regulated molecular mechanisms.

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021 (preprint)

Background The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just twenty six SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. Methods Nine hundred and five SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, gender, nationality and age. Results Although sixteen PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97% of samples. In the following two months, all samples contained the Alpha variant. However, this had changed dramatically by June and July, when all samples belonged to the Delta variant. Discussion This study provides a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country’s largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under six weeks.