SARS-CoV-2 Variants Typing using Real-Time Reverse Transcription-PCR-Based Assays in Addis Ababa, Ethiopia
No Thumbnail Available
Date
2023-05
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Addis Ababa University
Abstract
Background: Severe Acute Respiratory Syndrome Coronavirus 2 is a single-stranded positiveRNA that possesses 30,000 base pair in diverse variants. Even though genomic sequencing is awell-established variant detection method; but due to its cost and longer result turnaround timeattributes less attractive for variant identification in resource-limited countries. These complexitiespose the need for RT-PCR based variant typing.
Objective: This study aimed to determine the type of SARS-CoV-2 variants in the first fourconsecutive COVID-19 waves using variant typing PCR in Addis Ababa, Ethiopia.
Methods: A cross-sectional study was conducted from nasopharyngeal samples source from EPHICOVID-19 biobank repository. Samples were randomly selected from the first four waves basedon their collection dates. A total of 641 NP samples were selected and tested for SARS Cov-2.RNA was extracted using Bioer NPA-32P instrument (Zhejiang, China) using the extraction kitfrom MagaBio Plus RNA Purification Kit II (Hangzhou, China). The SARS-CoV-2 detection carried out from 10 μl RNA and 20 μl RT-PCR fluorescent mix (Shenzhen, China). The Ct valueless than 38 considered positive per the manufacturer. B.1.617 Lineage and 6 S-gene mutation(Shenzhen, China) PCR kits used for variant typing.
Result: From the 374 total tested for variant detection, 267 (71.4%) were identified by the varianttyping kits. The remaining, 107(28.6%) were not classified by both variant detection kits. Alpha,Beta, Delta, and Omicron, were dominantly identified variants from wave one, two, three and four,respectively. Based on the WHO variant classification, Alpha variant was identified with highproportion from wave-1 but absent in wave-4. Similarly, Beta variant detected from wave 1 to 3with varied proportion but dominant in wave-2. Delta variant entirely identified from wave 3 and4; while dominantly identified in wave 3. Omicron was the dominant variant of wave 4. From thetotal identified positive study samples, 243/267 (91%) variants identified from samples had Ctvalues less than 30 in diagnostic RT-PCR. Besides to VOC; VOI also identified.
Conclusion: The study data demonstrated that RT-PCR type variants from confirmed SARSCoV-2-positive sample. RT-PCR based variant typing would provide additional screening opportunity;where sequencing opportunity is inaccessible. The assays could be implemented in laboratoriesthat perform SARS-CoV-2 molecular testing.
Description
Keywords
SARS-CoV-2 whole genome sequence variants Ct value, whole genome sequence, variants, Ct value