SARS-CoV-2 variants typing using real-time reverse transcription-PCR-based assays in Addis Ababa, Ethiopia
| dc.contributor.advisor | Desta,Kassu(M.Sc., PhD candidate) | |
| dc.contributor.advisor | Diriba,Regassa(M.Sc.) | |
| dc.contributor.advisor | Sisay,Abay (M.Sc., PhD candidate) | |
| dc.contributor.advisor | Abera,Adugna(M.Sc., PhD candidate) | |
| dc.contributor.advisor | Gebreegziabxier,Atsbeha(MSc) | |
| dc.contributor.author | G/Meskel,Wodneh | |
| dc.date.accessioned | 2024-11-28T09:52:59Z | |
| dc.date.available | 2024-11-28T09:52:59Z | |
| dc.date.issued | 2023-05 | |
| dc.description.abstract | Background: Severe Acute Respiratory Syndrome Coronavirus 2 is a single-stranded positive RNA that possesses 30,000 base pair in diverse variants. Even though genomic sequencing is a well-established variant detection method; but due to its cost and longer result turnaround time attributes less attractive for variant identification in resource-limited countries. These complexities pose the need for RT-PCR based variant typing. Objective: This study aimed to determine the type of SARS-CoV-2 variants in the first four consecutive COVID-19 waves using variant typing PCR in Addis Ababa, Ethiopia. Methods: A cross-sectional study was conducted from nasopharyngeal samples source from EPHI COVID-19 biobank repository. Samples were randomly selected from the first four waves based on 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 kit from 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 value less 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 variant typing 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 high proportion from wave-1 but absent in wave-4. Similarly, Beta variant detected from wave 1 to 3 with varied proportion but dominant in wave-2. Delta variant entirely identified from wave 3 and 4; while dominantly identified in wave 3. Omicron was the dominant variant of wave 4. From the total identified positive study samples, 243/267 (91%) variants identified from samples had Ct values 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 laboratories that perform SARS-CoV-2 molecular testing. | |
| dc.identifier.uri | https://etd.aau.edu.et/handle/123456789/3742 | |
| dc.language.iso | en_US | |
| dc.publisher | Addis Ababa University | |
| dc.subject | SARS-CoV-2 | |
| dc.subject | whole genome sequence | |
| dc.subject | variants | |
| dc.subject | Ct value | |
| dc.title | SARS-CoV-2 variants typing using real-time reverse transcription-PCR-based assays in Addis Ababa, Ethiopia | |
| dc.type | Thesis |